error: incorrect number of fields (1) input.bam:1
1
1
Entering edit mode
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!!

0
Entering edit mode
@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.