User: DVA

gravatar for DVA
DVA430
Reputation:
430
Status:
Trusted
Location:
United States
Last seen:
3 hours ago
Joined:
3 years, 7 months ago
Email:
s***********@gmail.com

Posts by DVA

<prev • 125 results • page 1 of 13 • next >
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Comment: C: Mask gtf file for cufflinks
... Do you know if my library is 3' rna seq library, what parameters should I alter with StringTie? Ideally, for 3' rna seq lib, transcript assembly is not needed for our DE analysis. Some default setting such as 200bps in -m, minimum length allowed for predicted transcripts,will be not relevant. What ...
written 10 days ago by DVA430
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Comment: C: Mask gtf file for cufflinks
... Yes absolutely. That is what I will do next. Thank you! ...
written 11 days ago by DVA430
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Comment: C: Mask gtf file for cufflinks
... Thanks a lot. I was trying to repeat a previous analysis done by a colleague. ...
written 11 days ago by DVA430
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Mask gtf file for cufflinks
... Is the ["-M" option][1] necessary when using Cufflinks? I understand it would prevent downstream analysis focusing on regions like rRNA, but could this be done at the very end after differential expression? Also, I could not find a mask gtf to download from USCS genome browser... Any advice please? ...
rna-seq written 11 days ago by DVA430
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Comment: C: HISAT2 tmo and rna-strandness options not working as expected
... Wooo thank you! This is of great help! ...
written 25 days ago by DVA430
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HISAT2 tmo and rna-strandness options not working as expected
... I am new to HISAT2 and trying to play around with its options. I found the following issues and would appreciate your advice: 1. I downloaded the genome_tran (for grch38) folder, and wanted to check out the option: --tmo. According to the [manual][1], it should "Report only those alignments within ...
rna-seq written 25 days ago by DVA430
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Comment: C: Reasons for polyA in RNA Seq Reads
... okay will do. Thank you for all the comments you provided to my questions recently. ...
written 6 weeks ago by DVA430
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Reasons for polyA in RNA Seq Reads
... In my poly A capture RNA sequencing fastq output, I noticed that about 20% of the reads contain poly A in the middle (or even close to the front). I would like to understand more on this, because with DNA fragments mostly >300bps and read length 100 bps, we were not expecting to see poly A show u ...
rna-seq written 6 weeks ago by DVA430
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Comment: C: Base pair order in sequencer vs in fastq
... Thank you for the confirmation! ...
written 6 weeks ago by DVA430
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Comment: C: Best way to trim PolyA in RNA Seq reads?
... I thought the adaptor is always showing up at the left of the reads... why they will not be at the same spot please? Sorry for all these questions, but I really want to understand it better. Thank you. ...
written 6 weeks ago by DVA430

Latest awards to DVA

Voter 6 weeks ago, voted more than 100 times.
Popular Question 3 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 3 months ago, created a question with more than 1,000 views. For Output all allele counts at each position using bcftools
Popular Question 3 months ago, created a question with more than 1,000 views. For Manually edit the flags in a sam file
Popular Question 4 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Centurion 4 months ago, created 100 posts.
Popular Question 8 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Appreciated 8 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Popular Question 8 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 9 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Popular Question 10 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Student 13 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 14 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Appreciated 15 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Good Question 15 months ago, asked a question that was upvoted at least 5 times. For Develop an R package for CRAN vs BioConductor
Student 15 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 17 months ago, created a question with more than 1,000 views. For Identify point mutations from each read in sam files
Student 17 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Student 23 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Scholar 23 months ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Illumina's HiSeq strange Phred quality score
Scholar 2.1 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
Supporter 2.1 years ago, voted at least 25 times.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?

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