User: Lila M
Lila M • 370
- Reputation:
- 370
- Status:
- Trusted
- Location:
- UK
- Last seen:
- 3 months ago
- Joined:
- 2 years, 6 months ago
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Posts by Lila M
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... Super quick! Thanks very much!! ...
written 3 months ago by
Lila M • 370
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... That exactly what I was looking for!
Thanks! ...
written 3 months ago by
Lila M • 370
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... I understand what you say. My concern is if there is an easy option to construct a GRange (ranges and strand) object using the complete Dmelanogaster genome, let's say something like that, in a fast way:
genes <- GRanges(seqnames=c("chr2L" , "chr2R" , "chr3L" , "chr3R" , "chr4" , "chrX ...
written 3 months ago by
Lila M • 370
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... Hi everybody,
I was wondering if there is any way to convert BSgenome object to GRange.
I'm using `library(BSgenome.Dmelanogaster.UCSC.dm3)`
and I want a GR object like this:
FBgn0000003 chr3R [ 2648220, 2648518] + | FBgn0000003
FBgn0000008 chr2R [18024494, 18060346] + | FBg ...
written 3 months ago by
Lila M • 370
• updated
3 months ago by
Devon Ryan ♦ 78k
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... sorry, my mistake. I've run STAR with `--outReadsUnmapped` in the original fastq.gz file, and the result is the same I get when run STAR without that parameter, so this is why I'm thinking that the genome that I am using for mapping should include rRNA. I hope a much smaller bam file for `non_ribo.f ...
written 4 months ago by
Lila M • 370
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... I've tried, but as I am using the whole genome, the rRNA should be included in the gtf because the size is exactly the same for both bam files. ...
written 4 months ago by
Lila M • 370
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... I think that is easier if I use the non_ribosomal.fastq.gz output from bbduk to do the mapping and perform the downstream analysis. ...
written 4 months ago by
Lila M • 370
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... I think so, because I've used the [Genome sequence (GRCh38.p10)][1] and Comprehensive gene annotation (gencode.v27.annotation.gtf)
[1]: https://www.gencodegenes.org/releases/current.html ...
written 4 months ago by
Lila M • 370
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... so how can I get only the mapped reads? ...
written 4 months ago by
Lila M • 370
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... Regarding this answer, apparently STAR has not ignore the rRNA, because after generating the bam file and run `samtools view Aligned.sortedByCoord.out.bam | cut -f1 |sort | uniq |wc -l` I get a total of `44795631` that I assume are the mapped reads. So STAR is not ignoring at all the rRNA, rigth? ...
written 4 months ago by
Lila M • 370
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