STAR RNA - Generate Wiggle Plots from already aligned BAM files

Question

[sarajeanne08]

Hi All,

Is it possible to re-run STAR RNA aligner to obtain wiggle plots on already aligned and sorted BAM files? Or do I need to re-align again to obtain this type of output? I really do not want to have to re-align - so I am open to other options.

Thank you!

[shunyip]

Maybe this post can help.

Answer 1

[Devon Ryan]

bamCoverage from deepTools would be the quickest method to do this. You can also have it output bigWig rather than wiggle files, which is generally preferable (you can directly load those in IGV, for example).

[sarajeanne08]

Do you know if Deeptools can handle paired end reads and strandedness? as I know Bedtools can't handle these properly.

Thank you!

[Devon Ryan]

It can handle that without a problem (full disclosure, I'm one of the developers).

[sarajeanne08]

Hi Devon,

Thank you so much for the Deeptools recommendation! It works so well and is easy.

Thanks again!

Answer 2

[lcscs12345]

See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631051/

STAR --runMode inputAlignmentsFromBAM \
--inputBAMfile Aligned.sortedByCoord.out.bam \
--outWigType bedGraph \
--outWigStrand Stranded

[sarajeanne08]

Hi Icscs,

Thank you for your help. I tried running those commands but ended up with a bug:

$ STAR --runMode inputAlignmentsFromBAM --inputBAMfile Aligned.sorted.out.trimmed.bam.dupesmarked.bam --outWigType bedGraph --outWigStrand Stranded
Feb 07 11:15:48 ..... Reading from BAM, output wiggle
BUG: alignment extends past chromosome in signalFromBAM.cpp