User: suzanne11

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suzanne110
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Posts by suzanne11

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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... I tried again with this file, but still the same error, so indeed something else might be the problem. htseq: 0.10.0 numpy 1.14.5 pysam 0.14.1 python version: 3.5.5 ...
written 10 months ago by suzanne110
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... The original gtf file I was using I downloaded from here: ftp://ftp.ensembl.org/pub/grch37/update/gtf/homo_sapiens/    thanks!  ...
written 10 months ago by suzanne110
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... Hi, I checked, and in the original file there were. As I am new to programming and didn't now an easy fix for this, I first tried by making a new GTF file with only the gene ids on chr1. So in this new file, there are no more gene identifiers that appear on multiple chromosomes (as it only contains ...
written 10 months ago by suzanne110
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Comment: C: DEXSeq: Error running dexseq_prepare_annotation.py
... Dear Alejandro, Thank you for your help. To test, I created a new gtf file only containing information from chromosome 1. However, the error keeps appearing.. Does someone have any clue what is going on? Best, Suzanne ...
written 10 months ago by suzanne110
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DEXSeq: Error running dexseq_prepare_annotation.py
... Hello all, I am trying to run dexseq_prepare_annotation.py, but keep receiving the same error:   File "dexseq_prepare_annotation.py", line 129     raise ValueError, "Same name found on two chromosomes: %s, %s" % ( str(l[i]), str(l[i+1]) ) My guess is the problem is inside the gtf file, which was ...
dexseq written 10 months ago by suzanne110 • updated 10 months ago by Alejandro Reyes1.6k

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