Does HTSeq accepts BAM files from Mapsplice?

[narges]

Hi,

I have BAM files from Mapsplice and I wanted to quantify the expression levels with HTSeq. But I received following error. Do you think it is regarding the aligner or what is the problem?

samtools view file.bam | htseq-count --stranded=no hg19/Annotation/Genes/genes.gtf > test.txt

Warning: Read file:8:2203:10838:61544/2 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted)
Error: 'itertools.chain' object has no attribute 'get_line_number_string'
[Exception type: AttributeError, raised in count.py:200]

Thanks in advance

[GenoMax]

I assume these are RNA-seq BAM's. See the note about Mapsplice SAM incompatibility in this note: https://cghub.ucsc.edu/docs/tcga/UNC...eq_summary.pdf

[narges]

I assume these are RNA-seq BAM's. See the note about Mapsplice SAM incompatibility in this note: https://cghub.ucsc.edu/docs/tcga/UNC...eq_summary.pdf

Yes, they are and I have seen the document. I assumed it is not possible to "reconstruct the fastq files using samtools" but not other purposes like "samtools view ...".
But is there an alternative pipeline rather than samtools for quantifying the expression levels of BAM files from Mapsplice?

[GenoMax]

I am checking with TCGA group for a solution.

[narges]

I am checking with TCGA group for a solution.

Many thanks for the help.

[GenoMax]

I have been told that you can use bedtools (coverageBed) with a BED format file. That should work with MapSplice generated BAM's.