Question: Best Tool To Visualize Expression Peaks From Smallrna-Seq Alignment
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gravatar for Tom A
6.3 years ago by
Tom A100
United States
Tom A100 wrote:

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.

bed alignment chip-seq rna-seq • 2.3k views
ADD COMMENTlink modified 6.3 years ago by Charles Warden7.8k • written 6.3 years ago by Tom A100
1
gravatar for Charles Warden
6.3 years ago by
Charles Warden7.8k
Duarte, CA
Charles Warden7.8k wrote:

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).

ADD COMMENTlink written 6.3 years ago by Charles Warden7.8k

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

ADD REPLYlink written 6.3 years ago by Tom A100

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.

ADD REPLYlink written 6.3 years ago by Tom A100

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.

ADD REPLYlink written 6.3 years ago by Charles Warden7.8k

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

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Charles Warden7.8k
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