Forum: Bioinformatics
05-10-2012, 08:04 AM
|
|
Replies: 16
Views: 9,717
I apologize if my tone sounded personal. My...
I apologize if my tone sounded personal. My intent was to invite discussion that would clarify the points of disagreement. You seemed not to accept the unanimous opinion of the other commentors...
|
|
Forum: Bioinformatics
05-08-2012, 06:54 AM
|
|
Replies: 31
Views: 7,140
It's the right files, but it looks like they...
It's the right files, but it looks like they misconfigured the processing of the basecall files. The index should appear after the colon on the read name line, and it doesn't. I'll agree with Sven...
|
|
Forum: Bioinformatics
05-02-2012, 09:56 AM
|
|
Replies: 16
Views: 9,717
Heisman points out that if you have different...
Heisman points out that if you have different samples you should align first, remove duplicates, then merge. You conclude that since you have just one sample, you need to merge first and then align....
|
|
Forum: Bioinformatics
04-30-2012, 08:17 AM
|
|
Replies: 16
Views: 9,717
|
|
Forum: Bioinformatics
04-20-2012, 03:07 PM
|
|
Replies: 5
Views: 1,528
|
|
Forum: Bioinformatics
04-20-2012, 11:31 AM
|
|
Replies: 5
Views: 1,528
|
|
Forum: Bioinformatics
04-20-2012, 09:16 AM
|
|
Replies: 5
Views: 1,528
|
|
Forum: Bioinformatics
04-20-2012, 08:21 AM
|
|
Replies: 13
Views: 3,737
|
|
Forum: Bioinformatics
04-20-2012, 07:19 AM
|
|
Replies: 7
Views: 2,658
The issue is how white space is being parsed by...
The issue is how white space is being parsed by bash. The script does it's own parsing, then parsing happens again when the command is executed. It sometimes takes some trial and error before I get...
|
|
Forum: Bioinformatics
04-19-2012, 12:05 PM
|
|
Replies: 7
Views: 2,658
try this:
q10="-q10"
bwa_opt="$q10...
try this:
q10="-q10"
bwa_opt="$q10 $bwa_ref"
command="$stampy -g $ref_genome -h $ref_genome -o $out --bwa=$bwa --bwaoptions='$bwa_opt' -M $seq1 $seq2"
|
|
Forum: Bioinformatics
04-18-2012, 07:48 AM
|
|
Replies: 13
Views: 3,293
The program is using solexa quality scores...
The program is using solexa quality scores (starting at 64) instead of sanger (starting at 33). According to the fastx website (http://hannonlab.cshl.edu/fastx_toolkit/index.html), support for...
|
|
Forum: Bioinformatics
04-13-2012, 07:51 AM
|
|
Replies: 3
Views: 1,357
|
|
Forum: Bioinformatics
04-13-2012, 07:40 AM
|
|
Replies: 3
Views: 1,357
I don't see any problem here. For example, the...
I don't see any problem here. For example, the first row of you results says chromosome PT_34_209 has reference allele T at position 159 and a C snp was observed with quality 7.8, and there is no...
|
|
Forum: Bioinformatics
04-10-2012, 01:37 PM
|
|
Replies: 9
Views: 6,551
|
|
Forum: Bioinformatics
03-28-2012, 03:11 PM
|
|
Replies: 4
Views: 2,324
|
|
Forum: Bioinformatics
03-28-2012, 01:55 PM
|
|
Replies: 14
Views: 10,347
It's possible that the space in...
It's possible that the space in "/home/lab/Desktop/linux files" is making trouble. Remove the space, or move the vcftools_0.1.8a directory to the Desktop, and try again.
|
|
Forum: Bioinformatics
03-28-2012, 01:41 PM
|
|
Replies: 8
Views: 9,051
You can use samtools mpileup to check read...
You can use samtools mpileup to check read coverage:
samtools mpileup -r chr6:28543200-28543220 file.bam
...looks at reads covering 28,543,200 to 28,543,220 of chromosome 6. If you have the...
|
|
Forum: Bioinformatics
03-28-2012, 01:24 PM
|
|
Replies: 2
Views: 2,970
While this can certainly be done with standard...
While this can certainly be done with standard awk, bioawk (https://github.com/lh3/bioawk), makes it a bit easier:
awk -c fastx '{printf("@Indx-%d\n%s\n+\n%s\n",cnt++,$seq,$qual)}' old.fastq >...
|
|
Forum: Bioinformatics
03-28-2012, 12:58 PM
|
|
Replies: 8
Views: 9,051
As you've discovered, bam files almost always...
As you've discovered, bam files almost always need to be sorted by coordinate.
IGV won't display reads until you've zoomed in a good deal. Have you tried that? Are you sure you have reads in the...
|
|
Forum: Bioinformatics
03-27-2012, 04:11 PM
|
|
Replies: 10
Views: 2,350
|
|
Forum: Bioinformatics
03-27-2012, 01:06 PM
|
|
Replies: 10
Views: 2,350
Going from pileup to bam is a theoretical...
Going from pileup to bam is a theoretical possibility, but I doubt anyone has taken the trouble to make it a reality. Even the best you could do would miss out on some information, like pairing. ...
|
|
Forum: Bioinformatics
03-23-2012, 01:20 PM
|
|
Replies: 20
Views: 3,266
|
|
Forum: Bioinformatics
03-02-2012, 06:46 AM
|
|
Replies: 4
Views: 3,199
|
|
Forum: Bioinformatics
03-02-2012, 06:05 AM
|
|
Replies: 4
Views: 3,199
|
|
Forum: Bioinformatics
02-24-2012, 08:22 AM
|
|
Replies: 3
Views: 5,559
|
