Question: error: incorrect number of fields (1) input.bam:1
1
11 months ago by
kspata10
kspata10 wrote:

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!!

modified 11 months ago by Martin Morgan ♦♦ 24k • written 11 months ago by kspata10
Answer: error: incorrect number of fields (1) input.bam:1
0
11 months ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

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.