Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds31k
Reputation:
31,180
Status:
Trusted
Location:
Seattle, WA USA
Website:
http://bitsumma.com/
Twitter:
AlexReynolds
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
11 years, 1 month ago
Email:
a************@gmail.com

One of the developers behind the fast BEDOPS suite, whose pug Zac is the bestest pug in the world.

Posts by Alex Reynolds

<prev • 2,645 results • page 1 of 265 • next >
0
votes
0
answers
208
views
0
answers
Comment: C: Segmentation fault (core dumped) error with bigWigAverageOverBed
... You could try splitting the BED file by chromosome: $ sort-bed INPUT.bed > INPUT.sorted.bed $ for CHR in `bedextract --list-chr INPUT.sorted.bed`; do bedextract ${CHR} INPUT.sorted.bed > INPUT.sorted.${CHR}.bed; done Then run your `bigWigAverageOverBed` step on each per-chromosome fi ...
written 8 days ago by Alex Reynolds31k
0
votes
0
answers
208
views
0
answers
Comment: C: Segmentation fault (core dumped) error with bigWigAverageOverBed
... Chromosome names have to match up to do operations. In other words, `1,chr1` will not match up with `chr1`, for example. Adjust your `awk` statement accordingly, so that you're not adding commas, numbers or other extraneous stuff to the chromosome field of `INPUT.bed`. ...
written 9 days ago by Alex Reynolds31k
0
votes
0
answers
208
views
0
answers
Comment: C: Segmentation fault (core dumped) error with bigWigAverageOverBed
... That looks like a pretty unusual bed file, where the chromosomes do not look formatted correctly, and it isn't sorted in a typical way. What do the chromosome names in the bigWig file look like? ...
written 10 days ago by Alex Reynolds31k
0
votes
2
answers
1.2k
views
2
answers
Comment: C: Apple M1 processor for bioinformactics
... A port of Linux compatible with the M1 is being worked on. More information here: https://www.patreon.com/marcan and here: https://asahilinux.org/ ...
written 11 days ago by Alex Reynolds31k
2
votes
1
answer
130
views
1
answers
Answer: A: How to check size of genome?
... Reads will overlap, so you can't simply count the lengths of reads. To count the number of unique bases over reads per chromosome for assembly `hg38`, for example, using BEDOPS, bash, awk, and UCSC Kent utilities: $ ASSEMBLY=hg38 $ bam2bed --reduced < reads.bam | bedmap --echo --bases-un ...
written 13 days ago by Alex Reynolds31k
0
votes
1
answer
90
views
1
answers
Comment: C: Samtools Faidx Error Message
... Great point. I don't track what versions of dynamic libraries that tools use. One more argument in favor of static binaries. ...
written 15 days ago by Alex Reynolds31k
0
votes
1
answer
90
views
1
answers
Comment: C: Samtools Faidx Error Message
... Perhaps some of the advice here might help for getting OpenSSL libraries installed and linked: https://gist.github.com/aklap/e885721ef15c8668ed0a1dd64d2ea1a7 ...
written 15 days ago by Alex Reynolds31k
0
votes
3
answers
123
views
3
answers
Answer: A: Venn Diagrams with labels
... There is also [biovenn.nl][1]. [1]: http://biovenn.nl/ ...
written 16 days ago by Alex Reynolds31k
2
votes
3
answers
124
views
3
answers
Answer: A: separate_rows, but keep related ones together
... You could use a Python script to do this easily: #!/usr/bin/env python import sys headers = None idx = 0 for line in sys.stdin: elems = line.rstrip().split('\t') if idx == 0: headers = elems sys.stdout.write(line) else: ...
written 18 days ago by Alex Reynolds31k
2
votes
1
answer
111
views
1
answers
Answer: A: MEME cannot handle 318 sequence?
... Get the total, summed length of the 318 sequences in your FASTA file, e.g. via https://www.danielecook.com/generate-fasta-sequence-lengths/ Set your `-maxsize` parameter to this value. More explicitly, the output of the [aforementioned one-liner][1] can be quickly piped to a second `awk` statement ...
written 20 days ago by Alex Reynolds31k

Latest awards to Alex Reynolds

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Good Answer 6 days ago, created an answer that was upvoted at least 5 times. For A: Vcf File --> Gene/Protein Mutation Information
Scholar 13 days ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar 18 days ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Epic Question 20 days ago, created a question with more than 10,000 views. For Getting list of chromosome names from indexed BAM file
Appreciated 20 days ago, created a post with more than 5 votes. For A: Sam To Bed File With Counter Column
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Sam To Bed File With Counter Column
Appreciated 5 weeks ago, created a post with more than 5 votes. For Cubemaker - visualize three-dimensional datasets via the web
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Sam To Bed File With Counter Column
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar 7 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Scholar 7 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Appreciated 8 weeks ago, created a post with more than 5 votes. For Cubemaker - visualize three-dimensional datasets via the web
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar 3 months ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Appreciated 4 months ago, created a post with more than 5 votes. For Cubemaker - visualize three-dimensional datasets via the web
Popular Question 4 months ago, created a question with more than 1,000 views. For Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
Appreciated 5 months ago, created a post with more than 5 votes. For A: Genomic coordinates for Cytogenetic bands with R
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2531 users visited in the last hour
_