Blank reads and coverage track after loading .sorted.bam

[Aimee]

Hi,

I'm having an issue with viewing my reads in IGV, even at maximal zoom. I've downloaded the binary version of IGV_2.3.59 and am running it via linux on a ubuntu machine. The reads I am trying to view have been simulated from a region of interest in the GRCh38.p2 Primary Assembly so I have loaded the hg38 genome tract. I think I have dealt with the chromosome name mismatch correctly with my alias file: hg38_alias.tab:
gi|568815579|ref|NC_000019.10|:54722240-54869913    chr19
and it appears the .sorted.bam file is being imported but the reads and coverage tracts are blank (see attached). I'm not getting any errors or warnings to indicate what might be the problem.

I know questions similar to this have been asked before and I apologise if this has in fact been answered but I haven't been able to find a response that resolves my problem.

Any help would be much appreciated!

Aimee

[Jim Robinson]

Hi,

The alias doesn't look correct, in particular the ":54722240-54869913" at the end.

I have on my to-do list to update this assembly with all aliases.

Jim

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[Aimee]

Alrighty, should I remove that additional bp range from the end of the chromosome name in the header of all my .bam files?

[Jim Robinson]

If that is literally the sequence name in your .bam files you should not remove it,  that is a very strange name  for a sequence that's why I thought it suspicious.   In fact it looks like a genomic range.   If your reads were aligned to a range of a contig or sequence you probably won't be able to resolve it with alias files alone.    Do you have the fasta used for the bam alignment?  If so just load it as a "genome" using Genomes > Load from file,  then load your bam.

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[Aimee]

Thanks Jim, I'll give that a go. Yes you are right - my reference is a genomic range. I used that specific range of Hg38 sequence to artificially generate sequencing reads, de novo assembled them and then aligned them back to the same original reference sequence to assess the accuracy of the assembly. I just want to have a look at this in IGV - it's like a preliminary in silico analysis. Sorry, I'm new to handling this kind of data, maybe this is a weird thing to do.

Aimee

[Jim Robinson]

Hi,

Its not weird but when you do that you will need to use the fasta the bams were aligned to as the reference,  essentially you have created a new reference.

Jim

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[Jim Robinson]

Also, its possible the aliasing worked just fine,  but the reads are all offset by 54722240  bases relative to chr19 of hg38.

On 8/19/15 6:01 PM, Aimee wrote:

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