Moderator: swbarnes2

gravatar for swbarnes2
swbarnes28.9k
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
Comment: C: Help with Output of FASTA Files From Excel
... 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 swbarnes28.9k
1
vote
0
answers
49
views
0
answers
Comment: C: bowtie2 giving 0% alignment rato across all samples
... Step 1; can you get the desired results without the loop construct? ...
written 12 hours ago by swbarnes28.9k
1
vote
1
answer
59
views
1
answers
Comment: C: How to have the count of reads mapping each transcript of a fasta file ?
... 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 swbarnes28.9k
0
votes
1
answer
59
views
1
answers
Comment: C: How to have the count of reads mapping each transcript of a fasta file ?
... 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 swbarnes28.9k
0
votes
0
answers
47
views
0
answers
Comment: C: correct header with samtools mpileup
... 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 swbarnes28.9k
0
votes
1
answer
43
views
1
answers
Answer: A: Possibility of mapping opposite strand
... 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 swbarnes28.9k
1
vote
1
answer
49
views
1
answers
Answer: A: cellranger: min gene count and UMI/cell filter?
... 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 swbarnes28.9k
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 swbarnes28.9k
0
votes
1
answer
92
views
1
answers
Answer: A: Interpretation of two PCA plots
... 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 swbarnes28.9k
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 swbarnes28.9k

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
Scholar 23 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 27 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 28 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 29 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Blast: Homology Or Similarity?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
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
Scholar 6 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
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
Scholar 7 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
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
Scholar 8 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
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
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Oracle 4 months ago, created more than 1,000 posts (questions + answers + comments).
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 5 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 5 months ago, created an answer that has been accepted. For A: Problem with FPKM values
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
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values

Help
Access

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