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Best Tool To Visualize Expression Peaks From Smallrna-Seq Alignment

Hello all,

Does anyone know of a good tool that can be used to visualize expression-abundance peaks, perhaps using the .BED file from a smRNA-Seq alignment along with a gene model?

Thanks in advance.

rna-seq alignment chip-seq bed
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updated by Charles Warden Charles Warden • written by Tom A • Tom A

1 answer

If your miRNA quantification was done after alignment to a reference genome (hg19, mm10, etc), then it should be straightforward to view the read coverage for any region in IGV using a sorted .bam file. Small RNAs may already be in the RefSeq track, but you can add an additional track (as a .bed file), as needed.

If the alignment was performed on a fasta file with only the small RNA sequences, you can index that reference to view in IGV, but I think viewing the alignment is less helpful (for example, I think there will probably only be one way for the read to align a mature miRNA).

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written by Charles Warden Charles Warden

Thanks. Yes, they were done using reference hg19 and I have a .bam file to work with. I will give IGV a shot.

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written by Tom A • Tom A

EDIT: When I try to upload my .bam file I receive the following message: "An index file is required for SAM & BAM files.", even though I am using the "hg18" reference built into IGV. I have even tried with "Human (b37)" but I get the same error. What am I missing? Thanks.

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written by Tom A • Tom A

the .bam file needs to be sorted and indexed (so, there should be a .bai file, which is the .bam index file).

You can do this with samtools, and I think you might even be able to do with with igvtools within IGV.

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written by Charles Warden Charles Warden

I thought I saw another comment...anyways, to clearify, you need to sort your .bam file. You should then index the .bam file. Just like the fasta index, it will be recognized by the file name.

In other words, if your sorted .bam file is called sampleID.sort.bam, then your index file will be sampleID.sort.bam.bai. Because of the name structure, IGV looks for the .bai file when you import the sampleID.sort.bam file

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written by Charles Warden Charles Warden

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