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Search: Posts Made By: Richard Finney
Forum: General 10-12-2018, 11:33 AM
Replies: 2
Views: 205
Posted By Richard Finney
check out "affymetrix array snp calling" output...

check out "affymetrix array snp calling" output formats and codes

SNP_A* are snp ids (which map to dbSNPS's rsIDS)

The code is probably ...
0=AA (homozygous for the reference allele)
...
Forum: Bioinformatics 10-05-2018, 05:59 AM
Replies: 1
Views: 139
Posted By Richard Finney
This does not "add to both ends", I think I need...

This does not "add to both ends", I think I need a little more information to do that.

Here's a solution that appends "N"s.
It's not R, it's an awk "one liner" (a long one liner) :

cat...
Forum: Bioinformatics 09-27-2018, 04:01 PM
Replies: 6
Views: 265
Posted By Richard Finney
You could do some quality checks and remove...

You could do some quality checks and remove duplicates and recalibrate; but if you are just starting off, just go ahead and assume the data is good and try and see if you can get a report on...
Forum: Bioinformatics 09-27-2018, 06:20 AM
Replies: 6
Views: 265
Posted By Richard Finney
You will probably want to do some variant calling...

You will probably want to do some variant calling on the bam files. This may include SNPS, fusions, amplification or deletions.

There are many tools to do this. Searching for these tools is...
Forum: Bioinformatics 09-26-2018, 04:19 PM
Replies: 6
Views: 265
Posted By Richard Finney
How many samples do you have? How did you align...

How many samples do you have?
How did you align the reads?
Are they tumor and normal samples?
Are looking for germline characteristics or somatic changes?
Forum: Bioinformatics 05-11-2018, 10:27 AM
Replies: 4
Views: 448
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: 448
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: 369
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: 369
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: 11
Views: 1,011
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: 13,144
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: 1,732
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: 1,428
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: 1,155
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: 3,613
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: 613
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: 577
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: 1,279
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: 2,481
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: 1,175
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: 2,171
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: 1,126
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: 1,217
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: 1,948
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: 1,753
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...
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