Hi,
I am trying to use STAR alignments as input to the HTSeq count tools suitable for either DESeq or DEXSeq.
The error I am getting is:
2181086 GFF lines processed.
Error occured when reading first line of sam file.
Error: ("SAM optional field with illegal type letter ':'", 'line 28 of file GRL1259_76_GAGATTCC_L005_R1_001_AT_QT.paire
R_aligned.sam.bam.sorted.bam.sam')
[Exception type: ValueError, raised in _HTSeq.pyx:1180]
This is the first line of the samfile, the 28th line looks similar with a different read.
HWI-1KL163:53:C2191ACXX:1:1204:19189:58727 99 1 155979169 255 51M = 155979289 171 CCTTCACTATGGCTGAGAGCAGGGCAGGATCCAGGAGAAAGTGGCCAAGGG CCCFFFFFHHHHHJJJJJJIJJJJJJJJIJJJJIJFHHJJJFHGIJJJJJJ NH:i:1 HI:i:1 AS:i:100 nM:i:0
I am using the following commands:
STAR --genomeDir $genome_DIR --runThreadN 12 --genomeLoad NoSharedMemory --outSAMmode Full --outFilterMismatchNmax 3 --outFilterMultimapNmax 5 --readFilesIn $align_FILES
samtools view -h file.bam -o file.bam.sam
python -m HTSeq.scripts.count -m intersection-strict -t exon -s no -i gene_id $BAM_NAME.sorted.bam.sam $GTF >$BAM_NAME.sorted.bam.sam.out
I am using samtools 0.1.19, HTSeq 0.5.4p3, STAR 2.3.0
Thanks,
Bob
I am trying to use STAR alignments as input to the HTSeq count tools suitable for either DESeq or DEXSeq.
The error I am getting is:
2181086 GFF lines processed.
Error occured when reading first line of sam file.
Error: ("SAM optional field with illegal type letter ':'", 'line 28 of file GRL1259_76_GAGATTCC_L005_R1_001_AT_QT.paire
R_aligned.sam.bam.sorted.bam.sam')
[Exception type: ValueError, raised in _HTSeq.pyx:1180]
This is the first line of the samfile, the 28th line looks similar with a different read.
HWI-1KL163:53:C2191ACXX:1:1204:19189:58727 99 1 155979169 255 51M = 155979289 171 CCTTCACTATGGCTGAGAGCAGGGCAGGATCCAGGAGAAAGTGGCCAAGGG CCCFFFFFHHHHHJJJJJJIJJJJJJJJIJJJJIJFHHJJJFHGIJJJJJJ NH:i:1 HI:i:1 AS:i:100 nM:i:0
I am using the following commands:
STAR --genomeDir $genome_DIR --runThreadN 12 --genomeLoad NoSharedMemory --outSAMmode Full --outFilterMismatchNmax 3 --outFilterMultimapNmax 5 --readFilesIn $align_FILES
samtools view -h file.bam -o file.bam.sam
python -m HTSeq.scripts.count -m intersection-strict -t exon -s no -i gene_id $BAM_NAME.sorted.bam.sam $GTF >$BAM_NAME.sorted.bam.sam.out
I am using samtools 0.1.19, HTSeq 0.5.4p3, STAR 2.3.0
Thanks,
Bob
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