Moderator: swbarnes2

gravatar for swbarnes2
swbarnes24.0k
Reputation:
4,030
Status:
Trusted
Location:
United States
Last seen:
3 hours ago
Joined:
6 years, 5 months ago
Email:
s********@gmail.com

about me

Posts by swbarnes2

<prev • 434 results • page 1 of 44 • next >
0
votes
2
answers
60
views
2
answers
Answer: A: Proper design for DESeq2 and other RNAseq general questions
... 20 libraries So that's 7 trees, six tissues from each, with one of the pollen samples dropping out for some reason, right? > However, I am not sure how to design the formula for DESeq2 since I > only have two replicates for pollen. That's not the problem. Your design is just "tissue". It' ...
written 5 hours ago by swbarnes24.0k
0
votes
1
answer
124
views
1
answers
Comment: C: Is there a tool or efficient method of confirming that a FASTQ file and BAM file
... If you have removed reads because they did not map, or because they were duplicates, you do not need software to tell you that your bam file does not contain all the reads of the original fastq. ...
written 12 hours ago by swbarnes24.0k
0
votes
3
answers
204
views
3
answers
Comment: C: How to convert NGS .tabular file to excel file?
... In which case, converting it's format won't help. The poster in that case will need to use R, or a database program. But the poster almost certainly does not need to actually convert their file to .xlsx format. ...
written 1 day ago by swbarnes24.0k
2
votes
3
answers
204
views
3
answers
Answer: A: How to convert NGS .tabular file to excel file?
... Have you tried just opening the output in Excel? It's likely just tab delimited text, Excel shouldn't have an issue with that. Just pay attention to what Excel does to your gene names. ...
written 1 day ago by swbarnes24.0k
0
votes
2
answers
107
views
2
answers
Answer: A: discrepancy between reads
... > Im thinking about the homologous chromosome maybe doesn't have the > deletion, or maybe DNA from multiple cells in one sample? Either explanation could be the right one. It might be tricky to know which is correct. ...
written 1 day ago by swbarnes24.0k
4
votes
2
answers
141
views
2
answers
Answer: A: Why do R1 and R2 compressed files have different size
... Yes. It's perfectly possible, even if the reads are the same length. One might have sequences that are a little more repetitive, and therefore more compressible. If they have the same number of lines, that's all that matters. It of course also possible to run gzip with different levels of compre ...
written 6 days ago by swbarnes24.0k
0
votes
1
answer
124
views
1
answers
Comment: C: Is there a tool or efficient method of confirming that a FASTQ file and BAM file
... Are you trying to confirm that the fastq and bam are an exact match, or is spotchecking a few entries good enough? Would agreement in the # of reads be sufficient? ...
written 7 days ago by swbarnes24.0k
1
vote
2
answers
109
views
2
answers
Answer: A: STAR set --sjdbOverhang value
... You know the manual says about sjdbOverhang > **In most cases, a generic value of 100 will work as well as the ideal** > **value.** http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf ...
written 8 days ago by swbarnes24.0k
1
vote
1
answer
129
views
1
answers
Comment: C: Discrepancy between Nextera PE illumina produced sequence vs Sanger sequence of
... If you want help, you need to provide images that help. You need to zoom in and show at least a dozen bases context on both sides of your problem. So your discrepancy is literally sitting on your reverse sanger primer? Did you use that reverse primer to do PCR prior to sanger sequencing? Does yo ...
written 8 days ago by swbarnes24.0k
2
votes
1
answer
129
views
1
answers
Answer: A: Discrepancy between Nextera PE illumina produced sequence vs Sanger sequence of
... I can't make heads or tails as to how your sanger data is supposed to correspond to your Illumina data. You need to zoom in on the region of interest, and show more flanking information. Aside from the obvious possibility of sample mix-up, are there more than just those two SNPs? Does the Illumin ...
written 8 days ago by swbarnes24.0k

Latest awards to swbarnes2

Teacher 6 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 6 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 8 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Blast: Homology Or Similarity?
Scholar 10 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: how to identify a sequencing sample's gender
Scholar 3 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
Scholar 4 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Voter 5 months ago, voted more than 100 times.
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
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
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
Teacher 7 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 7 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Scholar 7 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
Scholar 9 months ago, created an answer that has been accepted. For A: Problem with FPKM values
Teacher 9 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 9 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: 1655 users visited in the last hour