Moderator: swbarnes2
swbarnes2 ♦ 8.9k
- Reputation:
- 8,900
- Status:
- Trusted
- Location:
- United States
- Last seen:
- an hour ago
- Joined:
- 8 years, 6 months ago
- Email:
- s********@gmail.com
about me
Posts by swbarnes2
<prev
• 1,198 results •
page 1 of 120 •
next >
1
vote
1
answer
61
views
1
answers
... Your assumption is crazy. Bowtie will take the name of each sequence from the header of each sequence (the part after the ">"), not from the file name!
And you hardly need featureCounts to count up how many reads aligned to each sequence. samtools idxstats will do that. ...
written 7 hours ago by
swbarnes2 ♦ 8.9k
1
vote
0
answers
49
views
0
answers
... Step 1; can you get the desired results without the loop construct? ...
written 12 hours ago by
swbarnes2 ♦ 8.9k
1
vote
1
answer
59
views
1
answers
... When you align to a subset of what you know is there, it can force reads to align to places they really don't belong. Better to align to the whole reference, then filter out what you don't care about after.
Samtools idxstats will quickly give you a count of how many reads aligned to each sequence ...
written 2 days ago by
swbarnes2 ♦ 8.9k
0
votes
1
answer
59
views
1
answers
... It's still not clear to me what you are doing. This is DNASeq? RNASeq? Do you have assemblies or just bams? ...
written 2 days ago by
swbarnes2 ♦ 8.9k
0
votes
0
answers
47
views
0
answers
... Pileup files have no header. Bam files absolutely do have headers. You don't run samtools view on a pileup file. ...
written 3 days ago by
swbarnes2 ♦ 8.9k
0
votes
1
answer
43
views
1
answers
... Genes run forward and backwards, so of course even a stranded protocol will run both forward and backwards when compared to the genome.
Ask Illumina which way the strandedness goes, or look yourself at how the reads align compared to the direction of individual transcripts. ...
written 3 days ago by
swbarnes2 ♦ 8.9k
1
vote
1
answer
49
views
1
answers
... I don't see a way to do that filtering with cellranger, but it's very easy to do in Seurat. Maybe it's a mistake in their description.
The decision as to whether or not a cell barcode represents a real cell or just cruft should be based on UMI count, but cellranger handles that. They might just b ...
written 7 days ago by
swbarnes2 ♦ 8.9k
0
votes
1
answer
92
views
1
answers
Comment:
C: Interpretation of two PCA plots
... The decision as to which end of the PC is positive and which is negative is essense arbitrary. Someone could take your data, run it on their system, and their computer could decide the other way, based on tiny differences in the computing environment.
In both graphs, PC1 is showing the same tren ...
written 8 days ago by
swbarnes2 ♦ 8.9k
0
votes
1
answer
92
views
1
answers
... They don't look completely different to me. In the first PC, you have Group4 on one side, 2 and some 5 and 6 in the middle, and the rest of 6, 1, 3 and 5 on the other end.
You got something a little more interesting happening in PC2 in the lncRNAs, but it's still a pretty small % of the variance.
...
written 8 days ago by
swbarnes2 ♦ 8.9k
1
vote
2
answers
66
views
2
answers
Answer:
A: Trimmomatic trimming 3' bases
... Your question is rather terse, but if you want the last 20 bases gone, it looks like the option you want is CROP. ...
written 10 days ago by
swbarnes2 ♦ 8.9k
Latest awards to swbarnes2
Teacher
14 days ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
22 days ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Appreciated
4 weeks ago,
created a post with more than 5 votes.
For A: Blast: Homology Or Similarity?
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
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
Oracle
4 months ago,
created more than 1,000 posts (questions + answers + comments).
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 806 users visited in the last hour