Dear, SEQanswers community,
I faced issue with creation counting tables for RNA-seq data using HTSeq software.
Before I performed TopHat alignment (accepted_hints.bam) for 28 fastq files (single-end reads) and Cuffmerge assemble (merged.gtf).
This is script, that I used:
htseq-count --format bam --stranded no accepted_hits.bam /merged.gtf > htseq_out.txt
At the end of HTSeq output file I got a message:
33300000 SAM alignment records processed.
Error occured when processing SAM input (record #33301227 in file /media/olha/3CEBA24E475DF793/ALL_olha_2/A15/tophat_out/accepted_hits.bam):
reference_id -1 out of range 0<=tid<84
[Exception type: ValueError, raised in calignmentfile.pyx:642]
Any suggestions will be highly appreciated.
Olha
I faced issue with creation counting tables for RNA-seq data using HTSeq software.
Before I performed TopHat alignment (accepted_hints.bam) for 28 fastq files (single-end reads) and Cuffmerge assemble (merged.gtf).
This is script, that I used:
htseq-count --format bam --stranded no accepted_hits.bam /merged.gtf > htseq_out.txt
At the end of HTSeq output file I got a message:
33300000 SAM alignment records processed.
Error occured when processing SAM input (record #33301227 in file /media/olha/3CEBA24E475DF793/ALL_olha_2/A15/tophat_out/accepted_hits.bam):
reference_id -1 out of range 0<=tid<84
[Exception type: ValueError, raised in calignmentfile.pyx:642]
Any suggestions will be highly appreciated.
Olha
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