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Search: Posts Made By: seq_lover
Forum: Bioinformatics 05-31-2012, 03:46 PM
Replies: 4
Views: 1,585
Posted By seq_lover
Thanks Peter, It was way faster than I...

Thanks Peter,

It was way faster than I predicted.
Forum: Bioinformatics 05-31-2012, 02:37 PM
Replies: 4
Views: 1,585
Posted By seq_lover
Thanks Nils.

Thanks Nils.
Forum: Bioinformatics 05-31-2012, 01:36 PM
Replies: 4
Views: 1,585
Posted By seq_lover
BAM Header minor edit

Hi,

I have around 20 BAM files and each of them have proper bam header including RG ID, Sample, Library, Platform unit, Description and Platform. I was reading the GATK manual and just realized...
Forum: Bioinformatics 05-21-2012, 07:39 PM
Replies: 3
Views: 2,668
Posted By seq_lover
This is a bug in BWA. If you use -q it puts the...

This is a bug in BWA. If you use -q it puts the trimmed nucleotide read in the output SAM file but the quality sequence is not trimmed at all and thus there is a difference in the length of the read...
Forum: Bioinformatics 05-17-2012, 10:15 AM
Replies: 0
Views: 1,210
Posted By seq_lover
readgroup id, sample, library confusion

We recently sequenced a specific mouse strain. The sequencing data was generated on the 5500 XL platform from the same mate-pair library from a single male mouse liver. We had our sequencing done on...
Forum: Bioinformatics 05-11-2012, 01:59 PM
Replies: 2
Views: 2,040
Posted By seq_lover
BWA -n option

I have been trying to use BWA to align my solid reads. In the manual it has been mentioned that you can use the -n option to limit the number of mismatches allowed between reference genome and the...
Forum: Bioinformatics 04-27-2012, 11:22 AM
Replies: 2
Views: 3,327
Posted By seq_lover
Hey I thought I found the solution but I was wrong

Hi,

I am using the following samtool view command to output the information about properly placed mate pairs (solid) in the output bam file.

samtools view -b -f 67,131,179,115 old.bam > new.bam...
Forum: Bioinformatics 04-26-2012, 07:53 PM
Replies: 2
Views: 3,327
Posted By seq_lover
Hey I figured it out myself: The following...

Hey I figured it out myself:

The following commands works:
samtools view -b -f 67,131,179,115 old.bam > new.bam

I am sorry for not giving this enough try before posting. I will not delete the...
Forum: Bioinformatics 04-26-2012, 07:38 PM
Replies: 2
Views: 3,327
Posted By seq_lover
samtools view

Hi,

I am using samtools view -f option to output mate-pair reads that are properly placed in pair in the bam file.

My command is as follows: (67,131- first read, second read and 115,179 first ,...
Forum: Bioinformatics 04-26-2012, 02:58 PM
Replies: 3
Views: 1,269
Posted By seq_lover
I have similar questions in this post: ...

I have similar questions in this post:
http://seqanswers.com/forums/showthread.php?t=19537

I used the following tool to figure it out but I am not sure if all of my steps are right....
Forum: Bioinformatics 04-26-2012, 02:54 PM
Replies: 5
Views: 2,945
Posted By seq_lover
Hi, If you use BWA can you comment on my...

Hi,

If you use BWA can you comment on my questions. I mean "Am i using the correct flags" because when I used these flags my BAM file reduced from 18 gb to 4 gb. I dont care about the unmapped or...
Forum: Bioinformatics 04-26-2012, 09:50 AM
Replies: 5
Views: 2,945
Posted By seq_lover
Thanks for the reply. This is my first analysis...

Thanks for the reply. This is my first analysis so i am going extra careful.
Forum: Bioinformatics 04-25-2012, 04:22 PM
Replies: 5
Views: 2,945
Posted By seq_lover
BWA and SAMtools

Hello Everyone,

I used BWA to align SOLiD mate pair reads (60,60) with parameters -n 8(total mismatch) -l 25 (seed) and -k 2 (mismatch in seed). I am getting a good mapping rate of around 65%. I...
Forum: Bioinformatics 04-25-2012, 04:06 PM
Replies: 14
Views: 17,311
Posted By seq_lover
I assume kgulukota is trying to give example for...

I assume kgulukota is trying to give example for mate pair library (solid) and swbarnes2 is giving example for paired end (illumina). I think both of them are correct. Please correct me if I am wrong.
Forum: Bioinformatics 02-23-2012, 01:46 PM
Replies: 1
Views: 1,717
Posted By seq_lover
Copied from MAQ Documentation at...

Copied from MAQ Documentation at http://maq.sourceforge.net/qual.shtml

What is Mapping Quality?

In a probabilistic view, each read alignment is an estimate of the true alignment and is...
Forum: Bioinformatics 02-23-2012, 01:36 PM
Replies: 1
Views: 3,696
Posted By seq_lover
Lifescope comes with all the tertiary analysis...

Lifescope comes with all the tertiary analysis (SNP calling, indel, annotation) modules. They have a very nice mapping analysis. I was able to map ~75-85% of total reads to ref genome at mapping...
Forum: Genomic Resequencing 11-18-2011, 07:46 AM
Replies: 0
Views: 1,531
Posted By seq_lover
some basic queries (mapping)

Hi everyone,

I am newbie to sequencing analysis. I would be thankful if someone can answer these questions:-

1) What are uncallable bases in reads? Are these "N" thing in some reads. Because...
Forum: Bioinformatics 10-30-2011, 09:31 PM
Replies: 0
Views: 1,885
Posted By seq_lover
problem with running MAQ

I downloaded the MAQ and installed it as instructed in the manual. I moved the binary files to /home/user/bin directory and then I could run the maq commands from anywhere. i already converted...
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