User: Fwip

gravatar for Fwip
Fwip490
Reputation:
490
Status:
Trusted
Location:
United States
Last seen:
3 months ago
Joined:
8 years, 1 month ago
Email:
p********@gmail.com

~

Posts by Fwip

<prev • 39 results • page 1 of 4 • next >
0
votes
1
answer
2.7k
views
1
answers
Comment: C: How to convert fastq to cram, and from cram back to fastq
... The -@ 4 option means to use 4 additional processing threads when decoding the CRAM file. It won't change the result, just speed it up on multi-core systems. ...
written 11 months ago by Fwip490
1
vote
2
answers
2.4k
views
2
answers
Comment: C: Separate Bam File
... You can specify the chromosome you want: ``` samtools view my.bam chr1:60000-120000 | your_awk_command samtools view my.bam chr1:120000-180000 | your_awk_command samtools view my.bam chr1:180000-240000 | your_awk_command ... samtools view my.bam chr2:60000-120000 | your_awk_command samtools view my ...
written 5.9 years ago by Fwip490 • updated 4 months ago by RamRS25k
1
vote
2
answers
3.4k
views
2
answers
Answer: A: Build Phylogenetic Trees From Bam Files
... I've found more success with [the POPBAM source from github](https://github.com/dgarriga/POPBAM). (I used commit `0cdbacc2fd869e0b65a64bf5ff38ca1c21f41657`) The important thing to note, though, is the header adjustment you need to do in order for POPBAM to recognize your samples. From http://popbam ...
written 6.0 years ago by Fwip490 • updated 8 weeks ago by RamRS25k
0
votes
1
answer
2.5k
views
1
answers
Comment: C: Help In Standaloneblast Bioperl
... Glad you got it working! I was hoping to write out a more detailed guide, but was pressed for time. ...
written 6.2 years ago by Fwip490
1
vote
1
answer
2.5k
views
1
answers
Answer: A: Help In Standaloneblast Bioperl
... The last line is running the blast program on the command line, then passing the result to a function that doesn't exist. This is definitely not how you use it. Check the documentation here: http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/StandAloneBlast.pm or here for StandAloneBlastP ...
written 6.2 years ago by Fwip490
1
vote
3
answers
15k
views
3
answers
Answer: A: Is There A Way To Run Fastqc On All The Fastq Files In The Different Directories
... At least on my version (0.10.1, apparently), fastqc will accept filenames listed on the command line. So, in the same vein as Pierre's answer, I would probably do: find -name '*.fq' -exec fastqc '{}' + ';' or find -name '*.fq' | xargs fastqc (I think the xargs way is a little easier for my brain t ...
written 6.2 years ago by Fwip490
0
votes
1
answer
9.9k
views
1
answers
Answer: A: Blastdbcmd - Too Many Positional Arguments <1>, The Offending Value: %F - Window
... Looking at the help, -entry_batch requires a filename after it from which to read each entry. Your command treats -outfmt as the file to be read from, so when it encounters the following "%f" it doesn't know what to do with it. ...
written 6.2 years ago by Fwip490
0
votes
2
answers
4.1k
views
2
answers
Answer: A: How To Generate A Smaller, Simpler Heatmap Similar To A Tile?
... Have you tried heatmap.2( ..., dendrogram = "none" ... ) to turn off the dendrogram? Remember to check ? heatmap.2 for usage info. ...
written 6.7 years ago by Fwip490
0
votes
3
answers
2.7k
views
3
answers
Comment: C: How To Compute The Number Of Reads In Bam That Overlap With A Region? The Overla
... Do you want to find reads that entirely contain a small region, or reads that are entirely within a region larger than the read? ...
written 6.9 years ago by Fwip490
1
vote
5
answers
8.0k
views
5
answers
Answer: A: Samtools Tview Problem
... I just ran into this issue. My problem was that the reference Fasta file contained a different name for the chromosome than the BAM file indicated. To fix it, I changed the Fasta header to match the one in the BAM file. In my case, samtools view -H in.bam | grep '@SQ' showed the name I should use ( ...
written 6.9 years ago by Fwip490

Latest awards to Fwip

Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Simple Redirection, I/O Problem With Bedtools
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Aligner That Preserves Case?
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Simple Redirection, I/O Problem With Bedtools
Appreciated 5.9 years ago, created a post with more than 5 votes. For Aligner That Preserves Case?
Voter 5.9 years ago, voted more than 100 times.
Supporter 5.9 years ago, voted at least 25 times.
Commentator 5.9 years ago, created a comment with at least 3 up-votes. For C: Calculating Tn (True Negatives) For An Indel Detection Method
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: What Is The Proper Way To Think About Reinventing The Wheel As A Bioinformaticia
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Simple Redirection, I/O Problem With Bedtools
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Reference Bias In Alignments
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Read Blast Output Directly From Stdout With Bioperl
Student 5.9 years ago, asked a question with at least 3 up-votes. For Aligner That Preserves Case?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1787 users visited in the last hour