Moderator: swbarnes2

gravatar for swbarnes2
swbarnes23.8k
Reputation:
3,800
Status:
Trusted
Location:
United States
Last seen:
7 hours ago
Joined:
6 years, 3 months ago
Email:
s********@gmail.com

about me

Posts by swbarnes2

<prev • 406 results • page 1 of 41 • next >
1
vote
3
answers
115
views
3
answers
Answer: A: Trim Paired-end Fastq Files
... Step one...ask the person who gave you the fatsq how they were filtered. The fastqs that came off the instrument should all be paired and in order. You might have fastqs where some reads were purged for quality reasons while their mates were left in the file. Or one was truncated. ...
written 1 day ago by swbarnes23.8k
0
votes
1
answer
66
views
1
answers
Comment: C: Reheadering a subsetted bam gives truncated file
... Are you sure that your header order of chromosomes really is the same order as no-mouse.bam? ...
written 3 days ago by swbarnes23.8k
0
votes
2
answers
99
views
2
answers
Comment: C: Bcl2fastq avoid addition of barcode to header
... Nope. No special options, no post processing. Version 2.19 if I remember right. Indices are included in the undetermined fastq file, but not the sample fastqs. Actually, I see that it depends on the instrument. I run the same version and command line of bcl2fastq on the Miseq, and I see indic ...
written 4 days ago by swbarnes23.8k
0
votes
2
answers
139
views
2
answers
Comment: C: Realign BAM files to other reference file
... You are saying that you filtered away huge numbers of reads with -F 4 without disturbing the read 1 and read 2 pairing? -F 12 would probably work, I'm really surprised that Picard took all those orphan reads in stride. ...
written 4 days ago by swbarnes23.8k
0
votes
2
answers
99
views
2
answers
Comment: C: Bcl2fastq avoid addition of barcode to header
... I trust the sample sheet to have that information correct. ...
written 5 days ago by swbarnes23.8k
0
votes
0
answers
47
views
0
answers
Comment: C: samtools mpileup `error uninitialized value $l in numeric lt` during BAM to FAST
... Shouldn't step one be to split out the piped parts into separate lines, so you at least know which command is at fault? Putting versions helps too...lots of people still using really old versions of samtools, ...
written 5 days ago by swbarnes23.8k
0
votes
2
answers
99
views
2
answers
Answer: A: Bcl2fastq avoid addition of barcode to header
... My fastqs have no barcodes in their header. (bcl2fastq v2.19.403) Only undetermined samples have that. ...
written 5 days ago by swbarnes23.8k
0
votes
2
answers
139
views
2
answers
Comment: C: Realign BAM files to other reference file
... Why is this superior to just using the original fastqs? ...
written 5 days ago by swbarnes23.8k
0
votes
2
answers
139
views
2
answers
Comment: C: Realign BAM files to other reference file
... The read group is not the problem. The problem is that bwa expects the first read of file one to be the mate of the first read of file 2. That assumption obviously does not hold throughout the whole file, because sorting by coordinates and throwing away reads ruins that. ...
written 7 days ago by swbarnes23.8k
1
vote
1
answer
97
views
1
answers
Answer: A: Faster processing of paired end FASTQ files
... Aligning to see if the adapter is there will be slow. There might not be a way around that. It might be faster to use a regex to look for exact matches, and align only the ones that fail the perfect regex match. Are you sure that there is no out of the box software that can do this for you? I'm ...
written 8 days ago by swbarnes23.8k

Latest awards to swbarnes2

Scholar 11 days ago, created an answer that has been accepted. For A: Problem with FPKM values
Commentator 12 days ago, created a comment with at least 3 up-votes. For C: how to identify a sequencing sample's gender
Scholar 8 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 11 weeks ago, created an answer that has been accepted. For A: Problem with FPKM values
Voter 3 months ago, voted more than 100 times.
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
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
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
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 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: Problem with FPKM values
Scholar 7 months ago, created an answer that has been accepted. For A: Problem with FPKM values
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
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
Teacher 12 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 13 months ago, created an answer with at least 3 up-votes. For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To B

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 523 users visited in the last hour