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Search: Posts Made By: nanto
Forum: Bioinformatics 05-31-2013, 10:53 AM
Replies: 0
Views: 887
Posted By nanto
Structural Variants in germline [WG trios up to 200x coverage]

Hi all,

I already checked the forum but did now find the answers.

I am about to find the germline SVs in sequenced trios. Therefore, I thought that it is a good idea to ask for a few tips on...
Forum: Bioinformatics 02-04-2013, 07:10 AM
Replies: 6
Views: 2,688
Posted By nanto
Yes, I remember, that somehow I did work out this...

Yes, I remember, that somehow I did work out this problem on my own.

I will try getting the instructions from my notes. Since that time a lot happends, but I'm pretty sure I didn't throw out sth,...
Forum: Bioinformatics 10-23-2012, 07:46 AM
Replies: 6
Views: 9,066
Posted By nanto
use: samtools view -S file.sam | awk '{print...

use:

samtools view -S file.sam | awk '{print $numberoffield}' > file

and just find which field is AS.
Forum: Bioinformatics 10-23-2012, 06:29 AM
Replies: 1
Views: 1,268
Posted By nanto
SAM HMM DNA alignment

After coming long way through blastn, and all of it's big family, to all kinds of burrows-wheeler aligners, now I'm interested in using HMM for dna alignment. I would use HMMER, but sequences are...
Forum: Bioinformatics 10-16-2012, 12:42 AM
Replies: 2
Views: 1,725
Posted By nanto
It depends how much coverage you have with those...

It depends how much coverage you have with those fastq reads. BWA will create substrings either way. Considering reads are of good quality you might want to use suggested parameters by the program....
Forum: Bioinformatics 10-11-2012, 06:23 AM
Replies: 12
Views: 5,038
Posted By nanto
so you have to dig in data from bwa. Check...

so you have to dig in data from bwa.

Check if reference is indexed and you are using this reference file in mpileup, use sorted bam file, make sure you have generated bam file with headers, count...
Forum: Bioinformatics 10-11-2012, 06:13 AM
Replies: 12
Views: 5,038
Posted By nanto
like i said mpileup makes some tricks, and also I...

like i said mpileup makes some tricks, and also I had problems with bwa-sw with long reads or large files (thought it was core dump but even on a big machine it failed) so i started using pileup...
Forum: Bioinformatics 10-11-2012, 01:36 AM
Replies: 6
Views: 1,455
Posted By nanto
funny thing is I know how it will look like, i...

funny thing is I know how it will look like, i just have to do it to visualize data.
Idea of length filtering and making per base qualities is good, i think i will use boxplots for each subset.
And...
Forum: Bioinformatics 10-11-2012, 01:07 AM
Replies: 6
Views: 1,455
Posted By nanto
no it's not one sequence. I received pretty new...

no it's not one sequence. I received pretty new data set, and sequence quality might be affected by it's length. I need some plots to show it. So I have to calculate average for each sequence with...
Forum: Bioinformatics 10-11-2012, 12:04 AM
Replies: 6
Views: 1,455
Posted By nanto
Hmm i must have forgotten to add part: please...

Hmm i must have forgotten to add part: please avoid posts: do it yourself.
Forum: Bioinformatics 10-11-2012, 12:02 AM
Replies: 12
Views: 5,038
Posted By nanto
it can generate pileup format if you're...

it can generate pileup format if you're interested in it. I'm using pileup format, cause I got used to parsing it in shell script :P But I was also doing some work with bcftools, but it's not very...
Forum: Bioinformatics 10-10-2012, 07:14 AM
Replies: 12
Views: 5,038
Posted By nanto
mpileup makes some tricks to people. I had so...

mpileup makes some tricks to people. I had so many problems with it, so I downloaded samtools version with pileup option. There should be no problems then.
Try samtools 0.1.15
Forum: Bioinformatics 10-10-2012, 06:20 AM
Replies: 6
Views: 1,455
Posted By nanto
read quality

I'm trying to retrieve average quality of each read to make graphs of read length/quality. I don't want to use fastx, fastqc, I want data to make graphs myself, so i can adjust scales. I retrieved...
Forum: Bioinformatics 10-02-2012, 04:16 AM
Replies: 2
Views: 2,154
Posted By nanto
blast to bam

Does anyone ever heard of anything that can convert bast output into sam or bam file? I'm doing all these analysis but I'm to lazy to figure out how to get the data from blast file that will match...
Forum: Bioinformatics 09-19-2012, 06:55 AM
Replies: 0
Views: 990
Posted By nanto
error profile plot

I'm doing quality control of my alignments from bwa-sw. I would like to make a error profile plot for that, but samstat does not generate one (with comparision on insertions, deletions and so on)....
Forum: Bioinformatics 09-18-2012, 01:41 AM
Replies: 2
Views: 1,910
Posted By nanto
I also heard that with extremely long reads...

I also heard that with extremely long reads bwa-sw can give not very reliable output. Is there any sense in browsing reads up to a given length, or it will change nothing, at will only consume my...
Forum: Bioinformatics 09-17-2012, 06:24 AM
Replies: 2
Views: 1,910
Posted By nanto
BWASW more reads in the output SAM file than in the input file

When running BWA I get normal total number of reads (the same as in the input file).

But when running BWASW alignment I get this:

(that's from samtools flagstat)

56125 + 0 in total...
Forum: Bioinformatics 09-12-2012, 07:47 AM
Replies: 6
Views: 2,688
Posted By nanto
PacBioToCA no output

I managed somehow to get frg files and so on.
But after this instruction:
./pacBioToCA -length 500 -partitions 200 -l pacbio -t 16 -s pacbio.spec -fastq pacbio.filtered_subreads.fastq illumina.frg...
Forum: Bioinformatics 09-11-2012, 04:27 AM
Replies: 0
Views: 708
Posted By nanto
amos tarchive2ca and CA problems, PB reads without sense

while trying to obtain frg file via tarchive2ca tool I receive a message:

ERROR: Cannot find the quality file corresponding to fasta./***

[/** - path to a file]

I named fasta, qual and xml...
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