Question: Visualizing pacbio-derived alignment in IGV
0
gravatar for cugopal
7 weeks ago by
cugopal0
cugopal0 wrote:

I have an alignment file (BAM) and an associated index file (pbi) delivered to me by the sequencing provider. I am trying to visualize the alignments in IGV (v2.8.0). I first tried to index the (sorted) BAM file using samtools as follows but it creates an empty index (bai) file.

samtools index alignment.bam

The resulting index file is essentially empty (16 bytes). Probably as a result, I don't see any information in the alignment track in IGV. (The FASTA file index, created with samtools faidx is fine).

IGV doesn't show anything when I indicate that the pbi file contains the index either.

How can I visualize the alignments?

bam pbi igv alignment • 105 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by cugopal0

That is the standard way of doing it. Is the BAM file ok? Are there mapped reads? Any error messages? Is the BAM sorted by coordinate?

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by ATpoint36k

PacBio BAM files can be of different types. Have you tried to see if the pbi index works? It seems to be an extension of usual .bai spec and IGV may understand it natively. Found a video here that shows IGV being used to visualize Sequel data.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by genomax87k

@ATpoint @genomax Yes, the BAM file only contains the reads, and not the alignment, which is what I assumed. Sorry. Thanks for your answers.

ADD REPLYlink written 7 weeks ago by cugopal0

No problem. Be sure to use bam2fastx tool from PacBio to convert your files to fastq reads.

ADD REPLYlink written 7 weeks ago by genomax87k

Thanks for the pointer to bam2fastx. Does it produce a different result from e.g. samtools fastq?

ADD REPLYlink written 7 weeks ago by cugopal0
1

If your BAM files has PacBio specific extensions that are referred to in the link above they may be lost by using plain samtools fastq.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by genomax87k
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