User: marina.v.yurieva
marina.v.yurieva • 520
- Reputation:
- 520
- Status:
- Trusted
- Location:
- Farmington, CT
- Scholar ID:
- Google Scholar Page
- Last seen:
- 9 months, 1 week ago
- Joined:
- 6 years, 3 months ago
- Email:
- m***************@gmail.com
Posts by marina.v.yurieva
<prev
• 118 results •
page 1 of 12 •
next >
2
votes
1
answer
316
views
1
answer
... I'm very sorry if this topic has been posted before, I couldn't find anything relevant.
I'm doing assembly with StringTie --merge using reference genome and the list of gtf files from my samples:
stringtie --merge -G ref.gtf -o merged.gtf assembly_gtf_list.txt
And for many known genes next to ...
written 14 months ago by
marina.v.yurieva • 520
• updated
6 days ago by
kristoffer.vittingseerup • 3.4k
0
votes
0
answers
326
views
0
answers
... Most of the data there is PE but there are some samples that are SE. Some of them are even from the same individuals, it's weird. I'm trying to compare tumor to normal tissue from the same individual and there are few of them with PE and SE reads samples as different biological samples. Read lengths ...
written 14 months ago by
marina.v.yurieva • 520
0
votes
0
answers
326
views
0
answers
... I'm trying to create a merged gtf from TCGA bam files with Stringtie --merge. But some of the files use SE reads and some - PE reads. Are those bam file compatible and can be used together to generate a new gtf? I tried to find this info in the manual and online but couldn't.
Thank you! ...
written 15 months ago by
marina.v.yurieva • 520
0
votes
1
answer
966
views
1
answers
... Does it overlap with another gene on an opposite strand? Maybe the reads are mapped there, not to your gene.
Also, you have your gene in the annotation file? Make sure it's not missing. ...
written 2.1 years ago by
marina.v.yurieva • 520
1
vote
1
answer
1.1k
views
1
answers
... It's working! Thank you SO much!!!
I used bamCoverage from deeptools:
bamCoverage -b sample.bam -of bedgraph --filterRNAstrand forward --samFlagExclude 16 --effectiveGenomeSize 2913022398 --normalizeUsing RPKM -o sample_plus.bedGraph
I'm not sure if it's enough to just use --filterRNAstrand ...
written 2.1 years ago by
marina.v.yurieva • 520
0
votes
0
answers
1.1k
views
0
answers
Comment:
C: bedGraph compress tools
... I tried bamCoverage. It worked really well, only had to play with the bin sizes a few times. Thank you! ...
written 2.1 years ago by
marina.v.yurieva • 520
0
votes
1
answer
1.1k
views
1
answers
... Yeah, I looked at everything, just gave the first example. Here is Gapdh:
![enter image description here][1]
[1]: https://s8.postimg.cc/vo83t6qpx/strand_error2.png ...
written 2.1 years ago by
marina.v.yurieva • 520
0
votes
1
answer
1.1k
views
1
answers
... Thank you! So should I remove the multi-mappers or filter on more specific tags? ...
written 2.1 years ago by
marina.v.yurieva • 520
7
votes
1
answer
1.1k
views
5 follow
1
answer
... I have stranded RNA-seq data which doesn't look stranded when I visualize bedGraphs in Genome Browser:
![enter image description here][1]
I tried different aligners (star, bowtie, bwa), different ways to make bedGraph files, nothing works. But when I run salmon on these samples, it detects ISR (pa ...
written 2.1 years ago by
marina.v.yurieva • 520
• updated
2.1 years ago by
Rob ♦ 4.2k
0
votes
0
answers
741
views
0
answers
... UCSC definitely takes Ensembl IDs but I don't remember if there should be ENSGXXXX.X or it doesn't need ".X" at the end.. ...
written 2.1 years ago by
marina.v.yurieva • 520
Latest awards to marina.v.yurieva
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Is there an ftp file upload for MG-RAST?
Scholar
12 months ago,
created an answer that has been accepted.
For A: How to download and Install samtools on Linux?
Scholar
12 months ago,
created an answer that has been accepted.
For A: pipeline for 16sRNA miseq illumina
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Is there an ftp file upload for MG-RAST?
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Is there an ftp file upload for MG-RAST?
Centurion
2.1 years ago,
created 100 posts.
Popular Question
3.7 years ago,
created a question with more than 1,000 views.
For Is there an ftp file upload for MG-RAST?
Popular Question
3.7 years ago,
created a question with more than 1,000 views.
For BWA MEM mapping issue
Popular Question
3.7 years ago,
created a question with more than 1,000 views.
For False negative SNPs and depth of coverage with sam/bcftools
Teacher
3.7 years ago,
created an answer with at least 3 up-votes.
For A: How to download and Install samtools on Linux?
Supporter
5.2 years ago,
voted at least 25 times.
Teacher
5.4 years ago,
created an answer with at least 3 up-votes.
For A: How to download and Install samtools on Linux?
Appreciated
5.7 years ago,
created a post with more than 5 votes.
For A: How to download and Install samtools on Linux?
Good Answer
5.7 years ago,
created an answer that was upvoted at least 5 times.
For A: How to download and Install samtools on Linux?
Scholar
5.7 years ago,
created an answer that has been accepted.
For A: pipeline for 16sRNA miseq illumina
Teacher
5.7 years ago,
created an answer with at least 3 up-votes.
For A: How to download and Install samtools on Linux?
Scholar
5.8 years ago,
created an answer that has been accepted.
For A: pipeline for 16sRNA miseq illumina
Scholar
5.9 years ago,
created an answer that has been accepted.
For A: pipeline for 16sRNA miseq illumina
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1681 users visited in the last hour