Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

Moderator: swbarnes2

gravatar for swbarnes2
swbarnes2 ♦ 6.9k
Reputation:
6,880
Status:
Trusted
Location:
United States
Last seen:
33 minutes ago
Joined:
7 years, 7 months ago
Email:
s********@gmail.com

about me

Posts by swbarnes2

<prev • 827 results • page 1 of 83 • next >
1
vote
0
answers
18
views
0
answers
Comment: C: samtools sort error
... `-o final output to stdout` looks like exactly what is happening. I used that ancient version for a long time, I'm pretty sure I used `> sorted.bam` ...
written 49 minutes ago by swbarnes2 ♦ 6.9k
1
vote
0
answers
18
views
0
answers
Comment: C: samtools sort error
... What version of samtools are you running? It looks like an older version that wants a ">" instead of "-o" to redirect output to a file instead of the terminal. ...
written 1 hour ago by swbarnes2 ♦ 6.9k
1
vote
3
answers
129
views
3
answers
Answer: A: Why you shouldn't normalize count data using gene-length AND library size for co
... Another problem with normalizations like TPM and RPKM is they will flatten out the raw read counts. Let's say you have a project where one sample has a gene with TPM of 0.5, and another sample has TPM of 1.0 Do those mean something like 2 reads versus 4 reads? Or more like 40 reads versus 80 read ...
written 7 days ago by swbarnes2 ♦ 6.9k
0
votes
1
answer
89
views
1
answers
Comment: C: Transcripts highly constitutively expressed
... What about picking genes with low p-values and very small fold changes? ...
written 8 days ago by swbarnes2 ♦ 6.9k
1
vote
1
answer
76
views
1
answers
Answer: A: multiple comparisons in DESeq2
... If your contrasts work, you don't have to worry about what ResultsNames shows you. And you can submit a contrast to lfcshrink, see the example at the bottom https://rdrr.io/bioc/DESeq2/man/lfcShrink.html I don't think you need that model.matrix line in there, and I'm not sure what that all() stat ...
written 12 days ago by swbarnes2 ♦ 6.9k
0
votes
1
answer
76
views
1
answers
Answer: A: Extract the sequence of a gene from an aligned BAM file
... You have the # of reads in the region, what more do you want? Can't you do the division yourself? ...
written 12 days ago by swbarnes2 ♦ 6.9k
4
votes
1
answer
108
views
1
answers
Answer: A: RPKM with bowtie output
... RSEM will take a bam file as input and return raw counts, RPKM and TPM ...
written 13 days ago by swbarnes2 ♦ 6.9k
0
votes
2
answers
125
views
2
answers
Comment: C: tool to analysis bulk RNAseq data with UMIs
... It pulls the UMI out of a read and puts it in the read name; That's not specific to scRNASeq ...
written 13 days ago by swbarnes2 ♦ 6.9k
1
vote
2
answers
125
views
2
answers
Answer: A: tool to analysis bulk RNAseq data with UMIs
... Have you looked at umi_tools? ...
written 13 days ago by swbarnes2 ♦ 6.9k
1
vote
2
answers
190
views
2
answers
Comment: C: Could you please explain Fold change, % of change, and log2 fold change (L2FC) t
... Read the labels of your second graph carefully. The x axis is not labeled log told change. ...
written 13 days ago by swbarnes2 ♦ 6.9k

Latest awards to swbarnes2

Teacher 11 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 11 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 4 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 6 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 9 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 9 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 9 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 9 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 9 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
Teacher 11 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
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
Scholar 3 months 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
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 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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Exon-Seq Mutation Detection
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 5 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: Bam to nucleotide frequencies
Scholar 6 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1768 users visited in the last hour