Question: STAR RNA - Generate Wiggle Plots from already aligned BAM files
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gravatar for sarajeanne08
3.3 years ago by
sarajeanne0810
sarajeanne0810 wrote:

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!

rna-seq • 2.9k views
ADD COMMENTlink modified 3.3 years ago by lcscs1234510 • written 3.3 years ago by sarajeanne0810

Maybe this post can help.

ADD REPLYlink written 3.3 years ago by shunyip180
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gravatar for Devon Ryan
3.3 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

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).

ADD COMMENTlink written 3.3 years ago by Devon Ryan95k
0
gravatar for sarajeanne08
3.3 years ago by
sarajeanne0810
sarajeanne0810 wrote:

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

Thank you!

ADD COMMENTlink written 3.3 years ago by sarajeanne0810

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. This comment belongs against @Devon's answer above.

ADD REPLYlink written 3.3 years ago by genomax83k

I tried to do this but my phone I guess messed up... I will delete it for now until I can fix it

ADD REPLYlink written 3.3 years ago by sarajeanne0810

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

ADD REPLYlink written 3.3 years ago by Devon Ryan95k

Hi Devon,

Thank you so much! I really appreciate your help and suggestion.

Sara

ADD REPLYlink written 3.3 years ago by sarajeanne0810

Hi Devon,

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

Thanks again!

ADD REPLYlink written 3.3 years ago by sarajeanne0810
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gravatar for lcscs12345
3.3 years ago by
lcscs1234510
New Zealand
lcscs1234510 wrote:

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

STAR --runMode inputAlignmentsFromBAM \
--inputBAMfile Aligned.sortedByCoord.out.bam \
--outWigType bedGraph \
--outWigStrand Stranded
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by lcscs1234510

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

ADD REPLYlink written 3.3 years ago by sarajeanne0810
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