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GBCS
Je
Commits
fcde931e
Commit
fcde931e
authored
Jul 16, 2018
by
Charles Girardot
Browse files
Merge branch 'master' of git.embl.de:grp-gbcs/Je
parents
c2e22edd
e9754a8e
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12
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MIT_
LICENSE
.txt
→
LICENSE
View file @
fcde931e
Copyright 2016 GBCS-EMBL
MIT License
Copyright (c) 2016 GBCS-EMBL
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
associated documentation files (the "Software"), to deal in the Software without restriction,
...
...
@@ -11,4 +13,4 @@ The above copyright notice and this permission notice shall be included in all c
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
\ No newline at end of file
IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
README.md
0 → 100644
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fcde931e
# Je
The main public repository is at
[
github
](
https://github.com/gbcs-embl/Je/
)
where issues or pull request can be created.
Additional documentation and support can be found at http://gbcs.embl.de/je
## Installation
*
Install from the bioconda channel with
`` conda install -c bioconda je-suite ``
*
Or, download the
``je_<version>.tar.gz``
from the
``dist/``
directory and unpack
## The Je tool suite
Je currently offers 4 tools:
*
**je clip**
to remove UMIs contained in reads of fastq files that do not need sample demultiplexing
*
**je demultiplex**
to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not)
*
**je demultiplex-illu**
to demultiplex fastq files according to associated index files (contain the sample encoding barcodes).
Reads can additionally contain UMIs (inline)
*
**je markdupes**
to filter BAM files for read duplicates taking UMIs into account
### Distributions
*
``dist/``
contains the different Je versions for download
*
Bioconda
starting from version 1.2 je-suite can be installed through conda: https://anaconda.org/bioconda/je-suite
### Source
*
``src/shell/je``
is the wrapper script to call ``java -jar je_1.0_bundle.jar``
*
``src/galaxy/``
contains the Je wrappers for Galaxy
*
``src/test/``
holds the different test data
README.rst
deleted
100644 → 0
View file @
c2e22edd
Je
--
Additional documentation and support can be found at http://gbcs.embl.de/je
The Je tool suite
=================
Contains
++++++++
Je currently offers 4 tools :
**je clip**
to remove UMIs contained in reads of fastq files that do not need sample demultiplexing
**je demultiplex**
to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not)
**je demultiplex-illu**
to demultiplex fastq files according to associated index files (contain the sample encoding barcodes).
Reads can additionally contain UMIs (inline)
**je markdupes**
to filter BAM files for read duplicates taking UMIs into account
Distributions
++++++
dist/
contains the different Je versions for download
Source
++++++
src/shell/je
is the wrapper script to call ``java -jar je_1.0_bundle.jar``
src/galaxy/
contains the Je wrappers for Galaxy
src/test/
holds the different test data
\ No newline at end of file
src/galaxy/.shed.yml
View file @
fcde931e
...
...
@@ -5,7 +5,7 @@ description: The Je tool suite
name
:
je
owner
:
gbcs-embl-heidelberg
homepage_url
:
http://gbcs.embl.de/Je
remote_repository_url
:
https://git
.embl.de/grp-gbcs
/Je/tree/master/src/galaxy
remote_repository_url
:
https://git
hub.com/gbcs-embl
/Je/tree/master/src/galaxy
auto_tool_repositories
:
name_template
:
"
{{
tool_id
}}"
description_template
:
"
Wrapper
for
Je
tool:
{{
tool_name
}}"
...
...
src/galaxy/je
deleted
100755 → 0
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c2e22edd
#!/bin/sh
# Wrapper around je_1.1_bundle.jar
# where are we stored ?
DIR
=
"
$(
cd
"
$(
dirname
"
${
BASH_SOURCE
[0]
}
"
)
"
&&
pwd
)
"
# echo $DIR
# path to jar file to execute, this jar is supposed to be in the same dir as this script
JAR_FILE
=
$DIR
"/je_1.2_bundle.jar"
# set default _JAVA_OPTIONS
_JAVA_OPTIONS
=
${
_JAVA_OPTIONS
:-
'-Xmx4G -Xms256m'
}
export
_JAVA_OPTIONS
# uncomment to change logging level using your own log4j.xml found in $DIR file
# OPTS="-Dlog4j.configuration=file:$DIR/log4j.xml"
java
$OPTS
-jar
$JAR_FILE
"
$@
"
exit
$?
src/galaxy/je-clip.xml
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fcde931e
...
...
@@ -3,11 +3,12 @@
<macros>
<import>
macros.xml
</import>
</macros>
<expand
macro=
"requirements"
/>
<stdio>
<exit_code
range=
"1:"
level=
"fatal"
description=
"Tool exception"
/>
</stdio>
<
version_command>
echo '1.0'
</
version_command>
<command
interpreter=
"bash"
>
<
expand
macro=
"
version_command
"
/
>
<command>
<![CDATA[
je clip
...
...
@@ -85,8 +86,7 @@
</test>
</tests>
<help>
<help>
<![CDATA[
**What it does**
...
...
@@ -242,6 +242,6 @@ This is an exhaustive list of options::
Default value: null.
]]>
</help>
</help>
<expand
macro=
"citations"
/>
</tool>
src/galaxy/je-demultiplex-illu.xml
View file @
fcde931e
...
...
@@ -3,11 +3,12 @@
<macros>
<import>
macros.xml
</import>
</macros>
<expand
macro=
"requirements"
/>
<stdio>
<exit_code
range=
"1:"
level=
"fatal"
description=
"Tool exception"
/>
</stdio>
<
version_command>
echo '1.0'
</
version_command>
<command
interpreter=
"bash"
>
<
expand
macro=
"
version_command
"
/
>
<command>
<![CDATA[
je demultiplex-illu
...
...
@@ -93,8 +94,9 @@
<param
name=
"MM"
value=
"3"
/>
<param
name=
"MMD"
value=
"2"
/>
<param
name=
"Q"
value=
"20"
/>
<param
name=
"DIAG"
value=
"false"
/>
<output
name=
"METRICS_FILE_NAME"
file=
"illu_summary_PE.txt"
ftype=
"tabular"
lines_diff=
"4"
>
<param
name=
"DIAG"
value=
"false"
/>
<output
name=
"METRICS_FILE_NAME"
file=
"illu_summary_PE.txt"
ftype=
"tabular"
lines_diff=
"4"
/>
<output
name=
"DEMULTIPLEX_RESULTS"
ftype=
"tabular"
>
<discovered_dataset
designation=
"unassigned_1"
file=
"illu_unassigned_1_PE.txt"
/>
<discovered_dataset
designation=
"unassigned_2"
file=
"illu_unassigned_2_PE.txt"
/>
<discovered_dataset
designation=
"emb681m5_GGACTCCTCTCTCTAT_2"
file=
"emb681m5_GGACTCCTCTCTCTAT_2.txt"
/>
...
...
@@ -111,8 +113,7 @@
</test>
</tests>
<help>
<help>
<![CDATA[
**What it does**
...
...
@@ -124,6 +125,8 @@ Author: Charles Girardot (charles.girardot@embl.de).
Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
With contributions by: Mehmet Tekman (@mtekman)
------
**Know what you are doing**
...
...
@@ -423,6 +426,6 @@ This is an exhaustive list of options::
Default value: null.
]]>
</help>
</help>
<expand
macro=
"citations"
/>
</tool>
src/galaxy/je-demultiplex.xml
View file @
fcde931e
...
...
@@ -3,11 +3,12 @@
<macros>
<import>
macros.xml
</import>
</macros>
<expand
macro=
"requirements"
/>
<stdio>
<exit_code
range=
"1:"
level=
"fatal"
description=
"Tool exception"
/>
</stdio>
<
version_command>
echo '1.0'
</
version_command>
<command
interpreter=
"bash"
>
<
expand
macro=
"
version_command
"
/
>
<command>
<![CDATA[
je demultiplex
...
...
@@ -59,7 +60,8 @@
<param
name=
"type"
value=
"single"
/>
<param
name=
"input_1"
value=
"file_1_sequence.txt"
ftype=
"fastqsanger"
/>
<param
name=
"BARCODE_FILE"
value=
"barcodes_SE.txt"
ftype=
"tabular"
/>
<output
name=
"METRICS_FILE_NAME"
file=
"summary_SE.txt"
ftype=
"tabular"
lines_diff=
"4"
>
<output
name=
"METRICS_FILE_NAME"
file=
"summary_SE.txt"
ftype=
"tabular"
lines_diff=
"4"
/>
<output
name=
"DEMULTIPLEX_RESULTS"
ftype=
"tabular"
>
<discovered_dataset
designation=
"unassigned_1"
file=
"unassigned_1_SE.txt"
/>
</output>
</test>
...
...
@@ -73,10 +75,12 @@
<param
name=
"BM"
value=
"BOTH"
/>
<param
name=
"BRED"
value=
"false"
/>
<param
name=
"COLLECT_OUTPUTS"
value=
"false"
/>
<param
name=
"barcode_list_type_con"
value=
"text"
/>
<param
name=
"barcode_text"
value=
"sample1 CACTGT:GTATAG sample2 ATTCCG:TCCGTC sample3 GCTACC:TGGTCA sample4 CGAAAC:CACTGT"
/>
<output
name=
"METRICS_FILE_NAME"
file=
"summary_PE.txt"
ftype=
"tabular"
lines_diff=
"4"
>
<output
name=
"METRICS_FILE_NAME"
file=
"summary_PE.txt"
ftype=
"tabular"
lines_diff=
"4"
/>
<output
name=
"DEMULTIPLEX_RESULTS"
ftype=
"tabular"
>
<discovered_dataset
designation=
"unassigned_1"
file=
"unassigned_1_PE.txt"
/>
<discovered_dataset
designation=
"unassigned_2"
file=
"unassigned_2_PE.txt"
/>
<discovered_dataset
designation=
"sample4_CGAAACCACTGT_2"
file=
"sample4_CGAAACCACTGT_2.txt"
/>
...
...
@@ -89,10 +93,36 @@
<discovered_dataset
designation=
"sample1_CACTGTGTATAG_1"
file=
"sample1_CACTGTGTATAG_1.txt"
/>
</output>
</test>
</tests>
<test>
<!-- Repeat of previous but with collection outputs -->
<param
name=
"type"
value=
"paired"
/>
<param
name=
"input_1"
value=
"file_1_sequence.txt"
ftype=
"fastqsanger"
/>
<param
name=
"input_2"
value=
"file_2_sequence.txt"
ftype=
"fastqsanger"
/>
<param
name=
"BPOS"
value=
"BOTH"
/>
<param
name=
"BM"
value=
"BOTH"
/>
<param
name=
"BRED"
value=
"false"
/>
<param
name=
"barcode_list_type_con"
value=
"text"
/>
<param
name=
"barcode_text"
value=
"sample1 CACTGT:GTATAG sample2 ATTCCG:TCCGTC sample3 GCTACC:TGGTCA sample4 CGAAAC:CACTGT"
/>
<param
name=
"COLLECT_OUTPUTS"
value=
"true"
/>
<output_collection
name=
"COLLECTION_1"
type=
"list"
>
<element
name=
"sample1_CACTGTGTATAG_1.txt"
value=
"sample4_CGAAACCACTGT_1.txt"
/>
<element
name=
"sample3_GCTACCTGGTCA_1.txt"
value=
"sample3_GCTACCTGGTCA_1.txt"
/>
<element
name=
"sample2_ATTCCGTCCGTC_1.txt"
value=
"sample2_ATTCCGTCCGTC_1.txt"
/>
<element
name=
"sample1_CACTGTGTATAG_1.txt"
value=
"sample1_CACTGTGTATAG_1.txt"
/>
</output_collection>
<output_collection
name=
"COLLECTION_2"
type=
"list"
>
<element
name=
"sample4_CGAAACCACTGT_2.txt"
value=
"sample4_CGAAACCACTGT_2.txt"
/>
<element
name=
"sample3_GCTACCTGGTCA_2.txt"
value=
"sample3_GCTACCTGGTCA_2.txt"
/>
<element
name=
"sample2_ATTCCGTCCGTC_2.txt"
value=
"sample2_ATTCCGTCCGTC_2.txt"
/>
<element
name=
"sample1_CACTGTGTATAG_2.txt"
value=
"sample1_CACTGTGTATAG_2.txt"
/>
</output_collection>
</test>
</tests>
<help>
<help>
<![CDATA[
**What it does**
...
...
@@ -104,6 +134,8 @@ Author: Charles Girardot (charles.girardot@embl.de).
Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
With contributions by: Mehmet Tekman (@mtekman)
------
**Know what you are doing**
...
...
@@ -434,6 +466,6 @@ This is an exhaustive list of options::
Default value: null.
]]>
</help>
</help>
<expand
macro=
"citations"
/>
</tool>
src/galaxy/je-markdupes.xml
View file @
fcde931e
...
...
@@ -3,11 +3,12 @@
<macros>
<import>
macros.xml
</import>
</macros>
<expand
macro=
"requirements"
/>
<stdio>
<exit_code
range=
"1:"
level=
"fatal"
description=
"Tool exception"
/>
</stdio>
<
version_command>
echo '1.0'
</
version_command>
<command
interpreter=
"bash"
>
<
expand
macro=
"
version_command
"
/
>
<command>
<![CDATA[
je markdupes
...
...
@@ -182,8 +183,7 @@
</test>
</tests>
<help>
<help>
<![CDATA[
**What it does**
...
...
@@ -403,6 +403,6 @@ This is an exhaustive list of options::
to clear the default value.
]]>
</help>
</help>
<expand
macro=
"citations"
/>
</tool>
src/galaxy/je_1.2_bundle.jar
deleted
100644 → 0
View file @
c2e22edd
File deleted
src/galaxy/macros.xml
View file @
fcde931e
<macros>
<token
name=
"@VERSION_STRING@"
>
1.2
</token>
<token
name=
"@VERSION_STRING@"
>
1.2.1
</token>
<xml
name=
"requirements"
>
<requirements>
<requirement
type=
"package"
version=
"1.2"
>
je-suite
</requirement>
</requirements>
</xml>
<xml
name=
"version_command"
>
<version_command>
je version 2
>&
1 | tail -n 1
</version_command>
</xml>
<token
name=
"@single_or_paired_cmd@"
>
#if str( $library.type ) == "single":
...
...
@@ -19,8 +27,8 @@
<xml
name=
"paired_options"
>
<when
value=
"paired"
>
<param
name=
"input_1"
format=
"fastq,gz"
type=
"data"
label=
"FASTQ file #1"
/>
<param
name=
"input_2"
format=
"fastq,gz"
type=
"data"
label=
"FASTQ file #2"
/>
<param
name=
"input_1"
format=
"fastq,
fastq.gz,fastqsanger,fastqsanger.
gz"
type=
"data"
label=
"FASTQ file #1"
/>
<param
name=
"input_2"
format=
"fastq,
fastq.gz,fastqsanger,fastqsanger.
gz"
type=
"data"
label=
"FASTQ file #2"
/>
<yield
/>
<param
name=
"SAME_HEADERS"
type=
"boolean"
label=
"Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
...
...
@@ -29,7 +37,7 @@
falsevalue=
"false"
checked=
"false"
/>
</when>
<when
value=
"paired_collection"
>
<param
name=
"input_1"
format=
"fastq,gz"
type=
"data_collection"
collection_type=
"paired"
<param
name=
"input_1"
format=
"fastq,
fastq.gz,fastqsanger,fastqsanger.
gz"
type=
"data_collection"
collection_type=
"paired"
label=
"FASTQ Paired Dataset"
/>
<yield
/>
<param
name=
"SAME_HEADERS"
type=
"boolean"
...
...
@@ -62,18 +70,18 @@
<option
value=
"paired_collection"
>
Paired-end Dataset Collection
</option>
</param>
<when
value=
"single"
>
<param
name=
"input_1"
format=
"fastq,gz"
type=
"data"
label=
"FASTQ file"
/>
<param
name=
"I1"
type=
"data"
format=
"fastq,gz"
label=
"First Index File"
/>
<param
name=
"input_1"
format=
"fastq,
fastq.gz,fastqsanger,fastqsanger.
gz"
type=
"data"
label=
"FASTQ file"
/>
<param
name=
"I1"
type=
"data"
format=
"fastq,
fastq.gz,fastqsanger,fastqsanger.
gz"
label=
"First Index File"
/>
</when>
<expand
macro=
"paired_options"
>
<param
name=
"I1"
type=
"data"
format=
"fastq,gz"
label=
"First Index File"
/>
<param
name=
"I1"
type=
"data"
format=
"fastq,
fastq.gz,fastqsanger,fastqsanger.
gz"
label=
"First Index File"
/>
<conditional
name=
"I2_CONDITIONAL"
>
<param
name=
"I2_AVAILABLE"
type=
"select"
label=
"Do you have a second index file?"
>
<option
value=
"true"
>
Yes
</option>
<option
value=
"false"
selected=
"true"
>
No
</option>
</param>
<when
value=
"true"
>
<param
name=
"I2"
type=
"data"
format=
"fastq,gz"
label=
"Second Index File"
/>
<param
name=
"I2"
type=
"data"
format=
"fastq,
fastq.gz,fastqsanger,fastqsanger.
gz"
label=
"Second Index File"
/>
<expand
macro=
"bred_conditional"
/>
</when>
<when
value=
"false"
/>
...
...
@@ -90,7 +98,7 @@
<option
value=
"paired_collection"
>
Paired-end Dataset Collection
</option>
</param>
<when
value=
"single"
>
<param
name=
"input_1"
format=
"fastq,gz"
type=
"data"
label=
"FASTQ file"
/>
<param
name=
"input_1"
format=
"fastq,
fastq.gz,fastqsanger,fastqsanger.
gz"
type=
"data"
label=
"FASTQ file"
/>
</when>
<expand
macro=
"paired_options"
>
<yield
/>
...
...
@@ -186,7 +194,7 @@
<when
value=
"text"
>
<param
name=
"barcode_text"
type=
"text"
area=
"True"
size=
"10x30"
value=
"sample_name
\t
barcode
\n
"
label=
"Barcode List"
value=
"sample_name
<tab>
barcode"
label=
"Barcode List"
help=
"Barcode list format: one sample per line. First column is sample name and second is the
barcode, separated by tab or space. A third and fourth column can be used to specify the resulting
file names. See help below."
>
...
...
@@ -270,19 +278,19 @@ ${from_text_area}</configfile>
</xml>
<token
name=
"@demultiplexer_common_output_options_cmd@"
>
KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ
STATS_ONLY=${
adv_options.
STATS_ONLY}
#if str( $
adv_options.
DIAG ) == "true":
KEEP_UNASSIGNED_READ=$
{
KEEP_UNASSIGNED_READ
}
STATS_ONLY=${STATS_ONLY}
#if str( $DIAG ) == "true":
BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
#end if
</token>
<xml
name=
"demultiplexer_common_output_options"
>
<
param
name=
"KEEP_UNASSIGNED_READ"
type=
"boolean"
label=
"Keep unassigned reads (KEEP_UNASSIGNED_READ)"
truealue=
"true
"
falsevalue=
"false"
checked=
"true"
/>
<section
name=
"adv_options"
title=
"Advanced Options"
expanded=
"Fals
e"
>
<
!--<section name="output_options" title="Output Options" expanded="True">-->
<param
name=
"COLLECT_OUTPUTS"
type=
"boolean
"
truevalue=
"true"
falsevalue=
"false"
checked=
"false"
label=
"Output forward and reverse reads in dataset collections"
/>
<param
name=
"KEEP_UNASSIGNED_READ"
type=
"boolean"
label=
"Keep unassigned reads (KEEP_UNASSIGNED_READ)"
truevalue=
"true"
falsevalue=
"false"
checked=
"tru
e"
/
>
<param
name=
"DIAG"
type=
"boolean"
label=
"Output barcode match reporting file (DIAG)"
truevalue=
"true"
falsevalue=
"false"
checked=
"false"
help=
"This file will
...
...
@@ -292,7 +300,7 @@ ${from_text_area}</configfile>
<param
name=
"STATS_ONLY"
type=
"boolean"
label=
"Only produce metric and diagnostic reports (STATS_ONLY)"
truevalue=
"true"
falsevalue=
"false"
checked=
"false"
help=
"do not demultiplex."
/>
</section>
<!--
</section>
-->
</xml>
<token
name=
"@common_options_cmd@"
>
...
...
@@ -317,24 +325,36 @@ ${from_text_area}</configfile>
help=
"Set to empty or null for no replacement."
value=
":"
/>
<param
name=
"GZ"
type=
"
boolean"
hidden=
"true
"
label=
"Compress output (GZ)"
<param
name=
"GZ"
type=
"
hidden
"
label=
"Compress output (GZ)"
help=
"will result in fastq.gz files."
truevalue=
"true"
falsevalue=
"false"
checked=
"false"
/>
value=
"false"
/>
</xml>
<token
name=
"@demultiplexer_common_outputs_cmd@"
>
METRICS_FILE_NAME=$METRICS_FILE_NAME
</token>
<xml
name=
"demultiplexer_common_outputs"
>
<data
name=
"
METRICS_FILE_NAME
"
format=
"tabular"
label=
"Je-Demultiplex result"
>
<
!--<discover_datasets pattern="(?P<name>.*)\.txt" ext="fastqsanger"--
>
<data
name=
"
DEMULTIPLEX_RESULTS
"
format=
"tabular"
label=
"Je-Demultiplex result
placeholder"
hidden=
"true
"
>
<
filter>
COLLECT_OUTPUTS == False and STATS_ONLY == False
</filter
>
<discover_datasets
pattern=
"(?P<name>.*)\.txt"
directory=
"results"
visible=
"true"
ext=
"fastqsanger"
/>
</data>
<data
name=
"METRICS_FILE_NAME"
format=
"tabular"
label=
"Je-Demultiplex Metrics"
/>
<data
name=
"BARCODE_DIAG_FILE"
format=
"tabular"
label=
"Barcode statistics"
>
<filter>
(adv_options['DIAG'] == 'true')
</filter>
<filter>
DIAG
</filter>
</data>
<collection
name=
"COLLECTION_1"
type=
"list"
label=
"${tool.name} on ${on_string} : Reads_1"
>
<filter>
COLLECT_OUTPUTS and STATS_ONLY == False
</filter>
<discover_datasets
pattern=
"(?P<designation>.+_1\..+)"
ext=
"fastqsanger"
directory=
"results"
visible=
"false"
/>
</collection>
<collection
name=
"COLLECTION_2"
type=
"list"
label=
"${tool.name} on ${on_string} : Reads_2"
>
<filter>
COLLECT_OUTPUTS and STATS_ONLY == False
</filter>
<discover_datasets
pattern=
"(?P<designation>.+_2\..+)"
ext=
"fastqsanger"
directory=
"results"
visible=
"false"
/>
</collection>
</xml>
<xml
name=
"citations"
>
<citations>
<citation
type=
"doi"
>
10.1186/s12859-016-1284-2
</citation>
</citations>
</xml>
</macros>
src/galaxy/test-data/illu_summary_PE.txt
View file @
fcde931e
...
...
@@ -4,8 +4,8 @@ Processed Reads (pairs) 25
Assigned Reads (pairs) 10
Unassigned Reads (pairs) 15
# Individual sample read (pair) counts :
emb681m1 2
emb681m4 2
emb681m5 2
emb68
0
1m
2
2
emb681m
1
2
emb6801m1 2
emb6801m2 2
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