Hi,
Based on the STAR aligned bam files, I tried to generate the counts of RNA-seq data using htseq-count (version 0.5.1) tool by giving following command
htseq-count -m intersection-nonempty input_bam_file gtf_file > Sample1_count.txt
I am getting the following error
Error occured when reading first line of sam file.
Error: ('SAM line does not contain at least 11 tab-delimited fields.', 'line 1 of file input_bam_file')
[Exception type: ValueError, raised in _HTSeq.pyx:1220]
I am not certain if the problem is with STAR generated bam file or with htseq-count ?
Any help is appreciated
P.S: this is the STAR command given to create the bam file
STAR --genomeDir genome_Dir/genome_mm10 --runThreadN 8 --readFilesIn sample_file --outFilterIntronMotifs RemoveNoncanonical --outSAMmode Full --outStd SAM | samtools view -bS - > Sample1.bam
Based on the STAR aligned bam files, I tried to generate the counts of RNA-seq data using htseq-count (version 0.5.1) tool by giving following command
htseq-count -m intersection-nonempty input_bam_file gtf_file > Sample1_count.txt
I am getting the following error
Error occured when reading first line of sam file.
Error: ('SAM line does not contain at least 11 tab-delimited fields.', 'line 1 of file input_bam_file')
[Exception type: ValueError, raised in _HTSeq.pyx:1220]
I am not certain if the problem is with STAR generated bam file or with htseq-count ?
Any help is appreciated
P.S: this is the STAR command given to create the bam file
STAR --genomeDir genome_Dir/genome_mm10 --runThreadN 8 --readFilesIn sample_file --outFilterIntronMotifs RemoveNoncanonical --outSAMmode Full --outStd SAM | samtools view -bS - > Sample1.bam
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