Moderator: swbarnes2

gravatar for swbarnes2
swbarnes24.7k
Reputation:
4,710
Status:
Trusted
Location:
United States
Last seen:
2 hours ago
Joined:
6 years, 9 months ago
Email:
s********@gmail.com

about me

Posts by swbarnes2

<prev • 536 results • page 1 of 54 • next >
0
votes
1
answer
81
views
1
answers
Comment: C: samtools sort truncated
... If you want the file sorted, why not tell STAR to sort it? ...
written 7 hours ago by swbarnes24.7k
0
votes
2
answers
88
views
2
answers
Comment: C: Comparing stranded reads to unstranded reads
... Batch effect is far more than library depth. The same samples prepped in different hands will have slightly different gene expression values. That's just life in experimental science. ...
written 6 days ago by swbarnes24.7k
1
vote
2
answers
88
views
2
answers
Answer: A: Comparing stranded reads to unstranded reads
... If the two sets of samples were prepped at different places at different times, strandedness is likely just a part of the larger batch effect. ...
written 6 days ago by swbarnes24.7k
1
vote
0
answers
113
views
0
answers
Comment: C: RNA-Seq Differential gene expression
... My limited experience with doing STAR alignment inside of RSEM was that the baked-in STAR parameters were really stringent. ...
written 10 days ago by swbarnes24.7k
0
votes
1
answer
89
views
1
answers
Answer: A: How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a
... HISAT is a splice-aware aligner. You align to genomes, and it is smart enough to know that many reads will align with large gaps. If you look at the index generating step, it is making the index with the guidance of a gtf with genomic features annotated by genomic coordinates. ...
written 10 days ago by swbarnes24.7k
1
vote
1
answer
134
views
1
answers
Answer: A: Alignment loop using STAR
... It would help to know what the error is. If the issue isn't storage space, it might be RAM used while sorting. You might try adding this --limitBAMsortRAM 31000000000 To your STAR command line. ...
written 10 days ago by swbarnes24.7k • updated 10 days ago by RamRS20k
0
votes
0
answers
113
views
0
answers
Comment: C: RNA-Seq Differential gene expression
... But feeding the transcriptome file to RSEM and using the rounded expected counts from RSEM works fine too. It might work a bit better, because RSEM is smarter about reads which align to multiple features. ...
written 10 days ago by swbarnes24.7k
0
votes
0
answers
65
views
0
answers
Comment: C: mirdeep2: UMI information lost when reads are collapsed
... You might need to align to a genome with a regular aligner, use something like UMI_tools on that alignment, then put those reads through mirDeep2. ...
written 11 days ago by swbarnes24.7k
1
vote
1
answer
95
views
1
answers
Answer: A: Differential expression comparing two groups normalized to a third group
... > Ideally I would like to normalize the expression of groups 2 and 3 to > group 1, and then compare the expression of group 2 vs 3. I don't think you want to do this. You usually want to normalize all the samples together. In DESeq2, use the "contrast" option when running "results" to speci ...
written 11 days ago by swbarnes24.7k
1
vote
2
answers
116
views
2
answers
Answer: A: RNA-Seq:How to know RNA-seq data is Strand-Specific or not based on only fastq
... If the library prep kit information is included, you can know from that. But it's probably easier to align and gauge strandedness empirically. ...
written 11 days ago by swbarnes24.7k

Latest awards to swbarnes2

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 5 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 8 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 3 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Blast: Homology Or Similarity?
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: how to identify a sequencing sample's gender
Scholar 8 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 8 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 8 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Voter 9 months ago, voted more than 100 times.
Scholar 10 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 10 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 10 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Scholar 10 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1944 users visited in the last hour