error: incorrect number of fields (1) input.bam:1
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kspata ▴ 10
@kspata-18956
Last seen 3.8 years ago

Hi,

I am trying to parse a BAM file using readAligned. It gives me an error of incorrect number of reads. How can I resolve this error. My command is as follows. The BAM file was generated by aligning to reference fasta file using Bowtie2.

 

reads = readAligned("input.bam", type = "Bowtie")

 

Will appreciate any help!!

 

shortread readaligned • 632 views
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@martin-morgan-1513
Last seen 13 days ago
United States

Probably you want instead to explore GenomicAlignments::readGAlignments() and similar; readAligned() is for 'legacy' formats that you are unlikely to encounter in a modern analysis.

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