Question: error: incorrect number of fields (1) input.bam:1
1
gravatar for kspata
7 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!!

 

shortread readaligned • 246 views
ADD COMMENTlink modified 7 months ago by Martin Morgan ♦♦ 23k • written 7 months ago by kspata10
Answer: error: incorrect number of fields (1) input.bam:1
0
gravatar for Martin Morgan
7 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k 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.

ADD COMMENTlink written 7 months ago by Martin Morgan ♦♦ 23k
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