Question: DEXSeq showing error with .bam files from HISAT
0
gravatar for W. Gi
23 months ago by
W. Gi0
Germany
W. Gi0 wrote:

Dear all,

I was trying to process RNASeq data with DEXSeq and attempt to transform the .bam file generated by HISAT into a DEXSeq required .txt file with the following code. However this error message keeps showing. Could someone tell me what I should do and/or what more information I should provide here to solve this problem? Thank you very much.

 

python pyScripts/dexseq_count.py Homo_sapiens.GRCh38.90.DEXSeq.gff  /projects/users/SID100/SID100_S1_L001_sorted.bam SID100.txt

Traceback (most recent call last):

  File "pyScripts/dexseq_count.py", line 183, in <module>

    for a in reader( sam_file ):

  File "/opt/pkg/lib/python2.7/site-packages/HTSeq/__init__.py", line 536, in __iter__

    algnt = SAM_Alignment.from_SAM_line( line )

  File "_HTSeq.pyx", line 1276, in HTSeq._HTSeq.SAM_Alignment.from_SAM_line (src/_HTSeq.c:24611)

ValueError: ('SAM line does not contain at least 11 tab-delimited fields.', 'line 1 of file /projects/users/SID100_S1_L001_sorted.bam')

 

 

rnaseq dexseq hisat • 320 views
ADD COMMENTlink written 23 months ago by W. Gi0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 196 users visited in the last hour