Question: DEXSeq showing error with .bam files from HISAT
gravatar for W. Gi
23 months ago by
W. Gi0
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/ Homo_sapiens.GRCh38.90.DEXSeq.gff  /projects/users/SID100/SID100_S1_L001_sorted.bam SID100.txt

Traceback (most recent call last):

  File "pyScripts/", line 183, in <module>

    for a in reader( sam_file ):

  File "/opt/pkg/lib/python2.7/site-packages/HTSeq/", 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
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