SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 500
Search took 0.12 seconds.
Search: Posts Made By: Richard Finney
Forum: Bioinformatics 09-21-2017, 07:36 AM
Replies: 7
Views: 865
Posted By Richard Finney
/* how to compile: gcc -Wall -O2 -o longestseq...

/*
how to compile: gcc -Wall -O2 -o longestseq longestseq.c
example: ./longestseq example.fa

*/

#include <stdlib.h>
#include <string.h>
#include <stdio.h>
Forum: Bioinformatics 06-13-2017, 10:55 AM
Replies: 4
Views: 1,272
Posted By Richard Finney
No. Its' one of about 6 projects I could get...

No. Its' one of about 6 projects I could get done if I had 2 more hours a day.
I didn't get very far with it.

Though if I were doing it now I'd use webassembly.
Forum: Bioinformatics 05-30-2017, 11:14 AM
Replies: 5
Views: 516
Posted By Richard Finney
Check out: ...

Check out:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=align2seq

This used to be called "bl2seq". Just play around with it by supplying two...
Forum: General 05-19-2017, 09:22 AM
Replies: 14
Views: 1,622
Posted By Richard Finney
Virtual Memory is configurable in linux (but not...

Virtual Memory is configurable in linux (but not on the fly, at initial setup).
Often there is only a little virtual memory configured as once the system is using virtual memory, it's usually...
Forum: Bioinformatics 05-09-2017, 07:59 AM
Replies: 2
Views: 436
Posted By Richard Finney
Well. What's the number of genes used in the...

Well.

What's the number of genes used in the 60/40 ratio calculation of "other" genes?

NB: correlation != causation. Even if you get a p-value, it's not "proof".

You'll need to do careful...
Forum: Bioinformatics 05-05-2017, 02:07 PM
Replies: 1
Views: 410
Posted By Richard Finney
Check out "Genome in a Bottle" : ...

Check out "Genome in a Bottle" :
https://github.com/genome-in-a-bottle/giab_FAQ
Forum: General 11-13-2016, 08:25 PM
Replies: 1
Views: 1,133
Posted By Richard Finney
Look here : ...

Look here :
ftp://hgdownload.cse.ucsc.edu/goldenPath/dm6/database/
Forum: Bioinformatics 11-07-2016, 01:36 PM
Replies: 8
Views: 2,256
Posted By Richard Finney
Help page is here: ...

Help page is here:
http://45.56.125.191/help.html

This image for this is reproduced here :
http://i.imgur.com/FUQR3Bg.png
img src="http://i.imgur.com/FUQR3Bg.png"

Whole genomes are...
Forum: Bioinformatics 11-01-2016, 07:34 AM
Replies: 4
Views: 914
Posted By Richard Finney
Get this file :...

Get this file : ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

This command will do it :wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

NCBI used to promote the term "Entrez" in terms like...
Forum: Bioinformatics 10-12-2016, 07:52 AM
Replies: 9
Views: 1,797
Posted By Richard Finney
I like this bam2wig script ... just need samtools...

I like this bam2wig script ... just need samtools and awk ...

samtools depth -aa your.bam | awk '{if (prev!=$1) print "fixedStep chrom="$1" start="$2" step=1 span=1\n"$3; else print $3; prev=$1}'...
Forum: Bioinformatics 09-01-2016, 12:42 PM
Replies: 1
Views: 819
Posted By Richard Finney
zcat the bam file and check for errors ......

zcat the bam file and check for errors ... example ...

[email protected]:~$ file test.bam
test.bam: gzip compressed data, extra field

[email protected]:~$ samtools index test.bam
...
Forum: Bioinformatics 09-01-2016, 12:29 PM
Replies: 8
Views: 940
Posted By Richard Finney
for i in $(ls *.gz); do sn=`echo $i | sed...

for i in $(ls *.gz); do sn=`echo $i | sed 's/\.gz$//'`; zcat $i > $sn; done;
Forum: Genomic Resequencing 08-15-2016, 08:37 PM
Replies: 2
Views: 1,079
Posted By Richard Finney
get this file : ...

get this file : ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

example fetch from command line: wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

ungzip (decompress) this file.
...
Forum: Bioinformatics 08-04-2016, 10:17 AM
Replies: 6
Views: 1,395
Posted By Richard Finney
Comments on Software for Genomics

I have a list of software that our organization deploys. I usually concentrate on open source tools to analyze genomics data with notable execptions of novoalign and Excel.
I am looking for user...
Forum: Bioinformatics 07-14-2016, 09:49 AM
Replies: 1
Views: 787
Posted By Richard Finney
Quick follow up. The Genomics Data Commons...

Quick follow up.
The Genomics Data Commons folks got back with me and say that there is indeed some problems with traciing back to original barcode.

Here's some work arounds until their "graph...
Forum: Bioinformatics 07-12-2016, 12:43 PM
Replies: 1
Views: 787
Posted By Richard Finney
Genomics Data Commons

TCGA data seems to now live at the Geomics Data Commons: https://gdc.nci.nih.gov/

The data is "accessible" via a RESTful interface.

It appears to be a mishmash jammed into some kind of NOSQL...
Forum: Bioinformatics 07-11-2016, 08:13 AM
Replies: 10
Views: 1,388
Posted By Richard Finney
Just a guess. Put a slash "/" after the...

Just a guess.

Put a slash "/" after the "src"
Forum: Bioinformatics 07-06-2016, 03:00 PM
Replies: 2
Views: 616
Posted By Richard Finney
This ~might~ be it ... From the paper (...

This ~might~ be it ...

From the paper ( http://www.nature.com/nature/journal/v466/n7309/full/nature09290.html
) ... "Regulation of heterochromatic DNA replication by histone H3 lysine 27...
Forum: Bioinformatics 05-31-2016, 02:39 PM
Replies: 3
Views: 816
Posted By Richard Finney
Clarification: I actually don't know if the files...

Clarification: I actually don't know if the files suppliekd by 1000 genomes is a whitelist or a blacklist.
I just wanted to point out that a possible reason that Exac and 1000 genomes are different...
Forum: Bioinformatics 05-30-2016, 09:01 AM
Replies: 3
Views: 816
Posted By Richard Finney
There's a 1000 genomes "blacklist". zcat...

There's a 1000 genomes "blacklist".


zcat chr2.bed.gz | awk '{if (($2<=130949553)&&($3>=130949553)) print $0}'
chr2 130949531 130949598 pilot

zcat chr17.bed.gz | awk '{if...
Forum: Clinical Sequencing 05-23-2016, 07:41 PM
Replies: 1
Views: 1,403
Posted By Richard Finney
Check out genome in a bottle. ...

Check out genome in a bottle.

http://www.nist.gov/mml/bbd/ppgenomeinabottle2.cfm
Forum: Bioinformatics 05-13-2016, 07:22 AM
Replies: 2
Views: 643
Posted By Richard Finney
http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?vie...

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies&f=study&term=mouse+cancer&go=Go
Forum: Bioinformatics 05-10-2016, 01:37 PM
Replies: 7
Views: 727
Posted By Richard Finney
I think your suspecting a "bad "reference genome...

I think your suspecting a "bad "reference genome spot may be correct.
Forum: Bioinformatics 04-25-2016, 02:20 PM
Replies: 2
Views: 602
Posted By Richard Finney
There are seperate "assemblies" in each file ... ...

There are seperate "assemblies" in each file ...
cut -f13 g36 | sort | uniq -c | sort -n
1 group_label
6 c22_H2
24 DR53
548 c5_H2
3026 c6_QBL
3242 c6_COX
21405...
Forum: Bioinformatics 04-22-2016, 04:09 PM
Replies: 2
Views: 495
Posted By Richard Finney
Check out NCBI geo ... ...

Check out NCBI geo ...

http://www.ncbi.nlm.nih.gov/gds/?term=%28heart+or+cardiovascular%29+AND+%28differentiation%29+AND+%28mouse[organism]+OR+human[organism]%29
Showing results 1 to 25 of 500

 


All times are GMT -8. The time now is 07:03 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO