Question: How to align to genome and transcriptome coordinates at the same time with STAR?
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gravatar for Crispy
6 days ago by
Crispy0
Crispy0 wrote:

Hi everyone,

I am analyzing a Ribosome Profiling and RNA-Seq dataset. For the analysis I am trying to repeat another published pipeline. However there it says:

" Reads were aligned in genome and transcriptome coordinates with a splice-aware aligner (STAR, v2.5.3a14, inserting annotations on the fly: STAR --quantMode TranscriptomeSAM --alignIntronMin 20 --alignIntronMax 100000 --outFilterMismatchNmax 1 -- outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMismatchNoverLmax 0.04 -- sjdbOverhang 50. We used the EnsEMBL mouse genome assembly GRCm38.p6, where all non- coding regions were excluded, and all fully contained shorter CDSs were collapsed: gffread -C - M -K.

Later they also write:

"Finally, only reads mapping uniquely to only one genomic position as well as to the transcriptome were kept for analysis."

If I understand correctly they first modified the GTF file of GRCm38.p6 with gffread -C - M -K. Then they somehow mapped to both the genome and the transcriptome together. How is this done? Can't I only use one file for where to map the reads to in STAR? Why would someone do this and not only map to only the genome or the transcriptome? Or does this mean it was done once at a time, e.g. first mapping to the genome and then seperately in a second run map to the transcriptome?

Some suggestions would help a lot. Thank you.

ADD COMMENTlink written 6 days ago by Crispy0

Did you try just running the command line as they described it? Or looking up what all those options do?

ADD REPLYlink modified 6 days ago • written 6 days ago by swbarnes2310

those are just general options, not specific for the issue of parallel aligning...

ADD REPLYlink written 6 days ago by Crispy0

those are just general options, not specific for the issue of parallel aligning...

ADD REPLYlink written 6 days ago by Crispy0

This question doesn't have anything to do with Bioconductor. It would be better directed to a more general forum such as biostars or SEQanswers.

ADD REPLYlink modified 6 days ago • written 6 days ago by Gordon Smyth38k

I will post it to a different forum.

ADD REPLYlink written 6 days ago by Crispy0
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