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CGGOxford / Opossum

Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
GNU General Public License v3.0
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Opossum parameters for single-end reads? #7

Open messersc opened 5 years ago

messersc commented 5 years ago

Hi,

I was wondering which Opossum parameters I should set for single-end reads.

I think I need to set --ProperlyPaired to false, because it looks like I'm not getting any reads otherwise.

Any other things I should take into account? What would be the recommended way to run opossum and platypus on single-end RNA-seq data?

Thanks, Clemens

ibwoo commented 5 years ago

I'm also interested in an answer to this.

Additionally, though GitHub has tracked only a single release dating back to Dec 2016, you have probably noticed in the readme file the following update from 2017:

0.2

Released on February 23, 2017. Updated dependency to Pysam v0.10.0. Opossum now supports unpaired data and filters out unmapped reads. Bug fixes.

So I'd say to check that you've downloaded the latest code, which may not be the 'latest release'.

messersc commented 5 years ago

Hi,

I totally missed that. I was on https://github.com/BSGOxford/Opossum/commit/de259b45a35cd7d4c01dbb40d48d16c9118d76c4, which is newer than the 0.2 commit though.

Guess I will need to revisit my analysis.

Thanks, Clemens

laura-oikkonen commented 5 years ago

Hello and apologies for the late reply. I have moved on to another field and unfortunately don't have time to maintain the Opossum code any more. Opossum indeed supports single-end reads, please use the latest code which is fe8f72e committed on 10 Apr 2018. Best regards, Laura

Udaykage commented 4 years ago

**Hi Guys I am using opossum for pre-processing my rna-seq bam files for variant calling and I got some errors as below, could you please help me with what the error means and how to fix it.

ERROR: **_[E::hts_idx_push] Region 536872898..536872913 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6 Traceback (most recent call last): File "/apps/opossum/0.2/Opossum.py", line 2074, in main() File "/apps/opossum/0.2/Opossum.py", line 482, in main pysam.index(outputfile) File "/apps/python/2.7.13/lib/python2.7/site-packages/pysam/utils.py", line 75, in call stderr)) pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=samtools index: failed to create index for "A_genome_mapping_sample_1_secondroundAligned.opossum.output.bam": Numerical result out of range\n'

I am using opossum/0.2

Working on wheat samples with SE reads

Script used : Opossum.py --BamFile=calm.out.bam --SoftClipsExist=True --ProperlyPaired=False --OutFile=A_genome_mapping_sample_1_secondroundAligned.opossum.output.bam

Thanks in advance Uday**