Hi all,
I have a quick question:
How can I visualize aligned paired-end reads from RNAseq datasets in UCSC browser?
I already mapped the reads and assembled the transcripts with Tophat/Cufflinks but I'm not sure how to proceed to visualize the mappings
After sorting the BAM files and fixing the mate pairs, I tried to compute the coverage using the following commands:
genomeCoverageBed -bg -split -ibam F.T0.rep2-accepted_hits-fS.bam -g ~/conversion_util/chrom.hg19.sizes > F.T0.rep2-accepted_hits-fS.bg
bedGraphToBigWig F.T0.rep2-accepted_hits-fS.bg ~/conversion_util/chrom.hg19.sizes F.T0.rep2-accepted_hits-fS.bw
But I was not able to visualize properly the mappings. Here I paste a screenshot of how it looks like:
Do you know where is the mistake?
Thanks!
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written
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daniel.soronellas
Tophat returns splitted reads (reads covering splice junctions) with Ns.
Here is an example of how the CIGAR string can look like: 78M2523N22M
I actually don't know, how genomeCoverageBed works, but it looks like, it gives coverage to Ns.
Thanks for your clarification! I appreciate!
But how can I manage to visualize this paired-end mRNA using browser? There's another way to do it?
visualizing read pairs dependes on the tool, I don't know if the UCSC browsers allows that - but you can certainly do that in IGV by right-clicking and selecting the options accordingly
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The -split option should exclude the introns. What version of bedtools is this? The latest is 2.17.0
I had been using version 2.16 and didn't worked, but once I changed to version 2.17 worked fine! Thanks!