User: Lila M

gravatar for Lila M
Lila M 370
Reputation:
370
Status:
Trusted
Location:
UK
Last seen:
4 days, 15 hours ago
Joined:
2 years, 3 months ago
Email:
p*************@gmail.com

Posts by Lila M

<prev • 242 results • page 1 of 25 • next >
0
votes
1
answer
111
views
1
answers
Comment: C: Is possible to convert BSgenome object to GRange?
... Super quick! Thanks very much!! ...
written 10 days ago by Lila M 370
0
votes
1
answer
111
views
1
answers
Comment: C: Is possible to convert BSgenome object to GRange?
... That exactly what I was looking for! Thanks! ...
written 11 days ago by Lila M 370
0
votes
1
answer
111
views
1
answers
Comment: C: Is possible to convert BSgenome object to GRange?
... 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 11 days ago by Lila M 370
6
votes
1
answer
111
views
1
answer
Is possible to convert BSgenome object to GRange?
... 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 ...
bsgenome granges written 11 days ago by Lila M 370 • updated 11 days ago by Devon Ryan74k
0
votes
1
answer
279
views
1
answers
Comment: C: high % of reads mapped to multiple loci after STAR mapping
... 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 6 weeks ago by Lila M 370
0
votes
1
answer
279
views
1
answers
Comment: C: high % of reads mapped to multiple loci after STAR mapping
... 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 6 weeks ago by Lila M 370
0
votes
1
answer
279
views
1
answers
Comment: C: high % of reads mapped to multiple loci after STAR mapping
... 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 6 weeks ago by Lila M 370
0
votes
1
answer
279
views
1
answers
Comment: C: high % of reads mapped to multiple loci after STAR mapping
... 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 6 weeks ago by Lila M 370
0
votes
1
answer
279
views
1
answers
Comment: C: high % of reads mapped to multiple loci after STAR mapping
... so how can I get only the mapped reads? ...
written 6 weeks ago by Lila M 370
0
votes
1
answer
279
views
1
answers
Comment: C: high % of reads mapped to multiple loci after STAR mapping
... 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 6 weeks ago by Lila M 370

Latest awards to Lila M

Voter 3 months ago, voted more than 100 times.
Popular Question 5 months ago, created a question with more than 1,000 views. For how to compare 2 fasta sequences with perl
Popular Question 5 months ago, created a question with more than 1,000 views. For How to convert bedgraph to bigwig?
Scholar 8 months ago, created an answer that has been accepted. For A: How to plot a heat map for the top 30 differentially expressed genes.
Centurion 10 months ago, created 100 posts.
Supporter 10 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 918 users visited in the last hour