I am runing the TopHat. I found that the header line of the file "accepted_hits.sam"is as following:
@HD VN:1.0 SO:sorted
@PG TopHat VN:1.0.130
The file "accepted_hits.sam" does not working for Samtools.
I use the commond "./samtools view -S -t -X -o exampl.flag accepted_hits.sam", and got two errors:
The tag [ID] required for [PG] not present.
Segmentation fault..
According to suggestions from nilshomer, I changed the line "@PG ID:TopHat VN:1.0.13). The first error is gone.
So my problems:
1) Why my file "accepted_hits.sam" without "ID:"?
2) how to fix the second error?
Thanks
@HD VN:1.0 SO:sorted
@PG TopHat VN:1.0.130
The file "accepted_hits.sam" does not working for Samtools.
I use the commond "./samtools view -S -t -X -o exampl.flag accepted_hits.sam", and got two errors:
The tag [ID] required for [PG] not present.
Segmentation fault..
According to suggestions from nilshomer, I changed the line "@PG ID:TopHat VN:1.0.13). The first error is gone.
So my problems:
1) Why my file "accepted_hits.sam" without "ID:"?
2) how to fix the second error?
Thanks
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