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Forum: Bioinformatics 05-11-2018, 10:27 AM
Replies: 4
Views: 365
Posted By Richard Finney
16 GB should be fine. What is your command line?...

16 GB should be fine. What is your command line? How much free memory do you have? (not total memory).
Forum: Bioinformatics 05-10-2018, 06:58 PM
Replies: 4
Views: 365
Posted By Richard Finney
Your mac is out of memory. Close your other...

Your mac is out of memory.
Close your other programs and try again.
Forum: Bioinformatics 05-04-2018, 11:48 AM
Replies: 4
Views: 307
Posted By Richard Finney
NC_000016 is a name used for "chr16". This the...

NC_000016 is a name used for "chr16".
This the "official" name used at NCBI : https://www.ncbi.nlm.nih.gov/nuccore/NC_000016.10/

You have to convert the "NCBI name" to "chr" names (or vice ...
Forum: Bioinformatics 05-04-2018, 10:27 AM
Replies: 4
Views: 307
Posted By Richard Finney
Check your chromosome names. Are they "chr"...

Check your chromosome names.
Are they "chr" style in both bed and bam?
Forum: Bioinformatics 04-10-2018, 10:17 AM
Replies: 7
Views: 716
Posted By Richard Finney
Some Spanish researchers publish a "principal...

Some Spanish researchers publish a "principal isoforms" database:
http://appris.bioinfo.cnio.es/#/

From their paper ( https://academic.oup.com/nar/article/46/D1/D213/4561658 .
APPRIS 2017:...
Forum: Bioinformatics 03-01-2018, 04:17 PM
Replies: 17
Views: 12,888
Posted By Richard Finney
The "-l parameter " (i.e. "dash el") specifies a...

The "-l parameter " (i.e. "dash el") specifies a file of (genomic postions) OR (genomic ranges in bed format) to produce output for. Regions OR positions not specified are dropped (not produced in...
Forum: Bioinformatics 09-21-2017, 06:36 AM
Replies: 7
Views: 1,475
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, 09:55 AM
Replies: 4
Views: 1,377
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, 10:14 AM
Replies: 5
Views: 925
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, 08:22 AM
Replies: 15
Views: 2,644
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, 06:59 AM
Replies: 2
Views: 570
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, 01:07 PM
Replies: 1
Views: 535
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, 07:25 PM
Replies: 1
Views: 1,243
Posted By Richard Finney
Look here : ...

Look here :
ftp://hgdownload.cse.ucsc.edu/goldenPath/dm6/database/
Forum: Bioinformatics 11-07-2016, 12:36 PM
Replies: 8
Views: 2,432
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, 06:34 AM
Replies: 4
Views: 1,127
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, 06:52 AM
Replies: 9
Views: 2,061
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, 11:42 AM
Replies: 1
Views: 1,044
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, 11:29 AM
Replies: 8
Views: 1,178
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, 07:37 PM
Replies: 2
Views: 1,663
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, 09:17 AM
Replies: 6
Views: 1,686
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, 08:49 AM
Replies: 1
Views: 971
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, 11:43 AM
Replies: 1
Views: 971
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, 07:13 AM
Replies: 10
Views: 1,803
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, 02:00 PM
Replies: 2
Views: 757
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, 01:39 PM
Replies: 3
Views: 974
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...
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