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Search: Posts Made By: Alex Renwick
Forum: Bioinformatics 05-10-2012, 07:04 AM
Replies: 16
Views: 8,892
Posted By Alex Renwick
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, 05:54 AM
Replies: 31
Views: 6,757
Posted By Alex Renwick
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, 08:56 AM
Replies: 16
Views: 8,892
Posted By Alex Renwick
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, 07:17 AM
Replies: 16
Views: 8,892
Posted By Alex Renwick
Could you explain more what you mean by this? ...

Could you explain more what you mean by this? Typically, each read is aligned independently of others, then the results are merged for subsequent analysis.
Forum: Bioinformatics 04-20-2012, 02:07 PM
Replies: 5
Views: 1,357
Posted By Alex Renwick
The time will depend on how many reads you have. ...

The time will depend on how many reads you have. Probably several hours. BWA can be multithreaded to use all 8 CPUs. Mapping will probably take a day or two.
Forum: Bioinformatics 04-20-2012, 10:31 AM
Replies: 5
Views: 1,357
Posted By Alex Renwick
If the experiment was done well, lanes should not...

If the experiment was done well, lanes should not affect the data. Pool the data before recalibrating.
Forum: Bioinformatics 04-20-2012, 08:16 AM
Replies: 5
Views: 1,357
Posted By Alex Renwick
PCR duplicates could appear in different lanes,...

PCR duplicates could appear in different lanes, and it's all one sample so it should all have the sample Read Group. I would do it in this order: map each fastq file, merge bam files, remove...
Forum: Bioinformatics 04-20-2012, 07:21 AM
Replies: 13
Views: 3,423
Posted By Alex Renwick
I do a lot of shell scripts and make files, and...

I do a lot of shell scripts and make files, and this Bpipe looks like it will make my life much easier.

I have a problem using the torque queue. The process does not return after successfully...
Forum: Bioinformatics 04-20-2012, 06:19 AM
Replies: 7
Views: 2,408
Posted By Alex Renwick
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, 11:05 AM
Replies: 7
Views: 2,408
Posted By Alex Renwick
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, 06:48 AM
Replies: 13
Views: 2,938
Posted By Alex Renwick
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, 06:51 AM
Replies: 3
Views: 1,204
Posted By Alex Renwick
Again I'll say that there is no problem. In the...

Again I'll say that there is no problem. In the vcf format the entries are separated by tabs. A long entry (the chromosome, in this case) can make the columns look misaligned, but the downstream...
Forum: Bioinformatics 04-13-2012, 06:40 AM
Replies: 3
Views: 1,204
Posted By Alex Renwick
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, 12:37 PM
Replies: 9
Views: 6,250
Posted By Alex Renwick
"perform computer analysis to identify SNPs" is...

"perform computer analysis to identify SNPs" is vague. Ask your instructor for clarification.
Forum: Bioinformatics 03-28-2012, 02:11 PM
Replies: 4
Views: 2,164
Posted By Alex Renwick
By "fourth column" I suppose you mean "third...

By "fourth column" I suppose you mean "third column", since the fourth column of the pileup format is the count of reads covering the site. See pileup format...
Forum: Bioinformatics 03-28-2012, 12:55 PM
Replies: 14
Views: 9,963
Posted By Alex Renwick
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, 12:41 PM
Replies: 8
Views: 8,362
Posted By Alex Renwick
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, 12:24 PM
Replies: 2
Views: 2,628
Posted By Alex Renwick
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, 11:58 AM
Replies: 8
Views: 8,362
Posted By Alex Renwick
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, 03:11 PM
Replies: 10
Views: 2,157
Posted By Alex Renwick
There must be an easier way to get what you want...

There must be an easier way to get what you want than resurrecting a bam from pileup. You could look at the files upstream of the pileup and see if they can be translated to bam format, or, on the...
Forum: Bioinformatics 03-27-2012, 12:06 PM
Replies: 10
Views: 2,157
Posted By Alex Renwick
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, 12:20 PM
Replies: 20
Views: 3,062
Posted By Alex Renwick
Here's what I did to download and compile a new...

Here's what I did to download and compile a new version of samtools:


wget -O samtools-0.1.18.tar.bz2...
Forum: Bioinformatics 03-02-2012, 05:46 AM
Replies: 4
Views: 2,840
Posted By Alex Renwick
For me, the awk command doesn't work even from...

For me, the awk command doesn't work even from the command line. The single quotes prevent bash from expanding "chr$a" to (e.g.) "chr1". Awk is looking for the third column to literally match...
Forum: Bioinformatics 03-02-2012, 05:05 AM
Replies: 4
Views: 2,840
Posted By Alex Renwick
I don't have any help for why your script didn't...

I don't have any help for why your script didn't run, but I can tell you that
samtools can do what you want by itself.


for a in {1..22}; do
samtools view -b file.bam chr$a -o Chr$a.bam...
Forum: Bioinformatics 02-24-2012, 07:22 AM
Replies: 3
Views: 4,959
Posted By Alex Renwick
Does chr6_apd_hap1 appear in your reference file...

Does chr6_apd_hap1 appear in your reference file (hg19.fa)? If so, try regenerating the dictionary file. You can use picard's CreateSequenceDictionary.jar, or, probably, just delete hg19.dict and...
Showing results 1 to 25 of 44

 


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