Je issueshttps://git.embl.de/grp-gbcs/Je/-/issues2023-08-25T07:09:52Zhttps://git.embl.de/grp-gbcs/Je/-/issues/5Int overflow in creating jemultiplexer_out_stats.txt on slightly larger genomes2023-08-25T07:09:52ZCharles GirardotInt overflow in creating jemultiplexer_out_stats.txt on slightly larger genomeshttps://github.com/gbcs-embl/Je/issues/5https://github.com/gbcs-embl/Je/issues/5Charles GirardotCharles Girardothttps://git.embl.de/grp-gbcs/Je/-/issues/4Add an option to specify the fastq input format2018-03-08T09:15:13ZCharles GirardotAdd an option to specify the fastq input formatto avoid the wrappers to have to make local symlinks.
actually, it should be enough to have an option specifying in the input is gzipped or not (as for the fastq version, Je does not rely on file extension)to avoid the wrappers to have to make local symlinks.
actually, it should be enough to have an option specifying in the input is gzipped or not (as for the fastq version, Je does not rely on file extension)Charles GirardotCharles Girardothttps://git.embl.de/grp-gbcs/Je/-/issues/3tracking the number of removed duplicated reads in a SAM flag - je markdupes ...2017-11-10T15:38:42ZThomas Schwarzltracking the number of removed duplicated reads in a SAM flag - je markdupes removeduplicatesDear all,
thanks for the great je suite.
When using
```
je markdupes
```
with the option
```
REMOVE_DUPLICATES=True
```
it would be great for further analysis of read duplication, if the number of duplication would be stored in the ...Dear all,
thanks for the great je suite.
When using
```
je markdupes
```
with the option
```
REMOVE_DUPLICATES=True
```
it would be great for further analysis of read duplication, if the number of duplication would be stored in the BAM file as a flag.
Currently, we are using the flag to count for read occurances
```
"YB:<number of reads>"
```
to deal with that. YB would be one if the read is not duplicated, and 2, 3, 4, .. if it had duplications.
This enables users to do statistics on what regions are duplicated most and for certain sequencing types, what RNA types are duplicated by the protocol.
Thank you very much.https://git.embl.de/grp-gbcs/Je/-/issues/2Appending barcodes at the end of read names prevent Picard MarkDuplicates fro...2021-03-24T12:45:03ZCharles GirardotAppending barcodes at the end of read names prevent Picard MarkDuplicates from identifying any optical duplicatesHi Charles,
I just wanted to raise a potential issue with Je. The are two default parameters for Je that cause a potential issue for downstream processing. The default parameters are ADD=TRUE and SAME_HEADERS=TRUE. If you have a paired ...Hi Charles,
I just wanted to raise a potential issue with Je. The are two default parameters for Je that cause a potential issue for downstream processing. The default parameters are ADD=TRUE and SAME_HEADERS=TRUE. If you have a paired end read with the following header:
@NB501764:261:HMKKLAFXX:1:11101:3199:1031 1:N:0
This would be converted to
@NB501764:261:HMKKLAFXX:1:11101:3199:1031:BARCODE
Instead of
@NB501764:261:HMKKLAFXX:1:11101:3199:1031 1:N:0:BARCODE
Appending the barcode to cluster coordinates will prevent Picard MarkDuplicates from identifying any optical duplicates.
I hope that makes sense!
AdamCharles GirardotCharles Girardot2021-04-15https://git.embl.de/grp-gbcs/Je/-/issues/1je-demultiplex-illu does not handle UMI correctly2017-06-21T10:39:41ZCharles Girardotje-demultiplex-illu does not handle UMI correctlyour IT department provides the je-demultiplex-illu tool in the galaxy suite (toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex_illu/je_demultiplex_illu/1.0)
It has been working great, but in the newest sequence data I got...our IT department provides the je-demultiplex-illu tool in the galaxy suite (toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex_illu/je_demultiplex_illu/1.0)
It has been working great, but in the newest sequence data I got UMIs have been included at the start of the reads. When I activate the UMI option they are correctly removed from the reads, but not added into the headers. The IT department has informed me that the same issue exists in the console version. I already have a workaround by using your Je-Clip tool separately, I just wanted to let you know that the Je-demultiplex-illu tool is not handling the UMIs correctly (i.e. like the Je-Clip tool).
best regards and thank you for developing the tool, it has made my live much easier :)
Mark
--
Mark Heron (Ph.D. Student)
Soeding Lab (Protein Bioinformatics & Computational Biology)
Gene Center, University of Munich (LMU)
Feodor-Lynen-Strasse 25
81377 Muenchen, Germany
Email: heron@genzentrum.lmu.de
Phone: +49-89-2180-76731
Fax: +49-89-2180-76797
Web: http://www.soeding.genzentrum.lmu.de/
https://www.mpibpc.mpg.de/soedingCharles GirardotCharles Girardot