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Forum: Bioinformatics 07-16-2013, 10:54 AM
Replies: 0
Views: 1,727
Posted By nupurgupta
bwa-mem and quality trimming

I want to switch from using bwa aln+sampe to bwa-mem, but I notice that there is no quality soft-trimming in the latter. (It is present in bwa aln). Am I missing something? Why has it not been...
Forum: Genomic Resequencing 03-05-2013, 12:49 PM
Replies: 21
Views: 16,386
Posted By nupurgupta
Same problem

Did you find a solution to the null problem please?
Forum: Bioinformatics 07-26-2012, 07:31 AM
Replies: 3
Views: 3,067
Posted By nupurgupta
Oh dear..I think the current version of samtools...

Oh dear..I think the current version of samtools doesnt even support it. Do you know which version you were using, I will get that
Thanks very much!
Forum: Bioinformatics 07-24-2012, 07:21 AM
Replies: 3
Views: 3,067
Posted By nupurgupta
vcfutils to get consensus sequence

There have been several posts about this, but it has been a while, and my queries are not completely answered, so thought I would put it down again.

I am trying to generate a consensus sequence...
Forum: Bioinformatics 07-24-2012, 07:12 AM
Replies: 5
Views: 6,682
Posted By nupurgupta
I am trying to understand how to set $q. In the...

I am trying to understand how to set $q. In the line

$q = $1 if ($t[7] =~ /FQ=(-?[\d\.]+)/);

Does it mean get $q from command line (1st paramter) in case there is an FQ value?

Thanks very...
Forum: Bioinformatics 07-24-2012, 06:49 AM
Replies: 9
Views: 9,384
Posted By nupurgupta
Yeah, except that vcfutils has an error if your...

Yeah, except that vcfutils has an error if your VCF entry doesn't have an FQ value. Which is true in current format of VCF. And I don't feel comfortable modifying the vcfutils.pl file. So if anyone...
Forum: Bioinformatics 07-24-2012, 06:47 AM
Replies: 1
Views: 3,718
Posted By nupurgupta
Hi, Did you finally figure this out, and write...

Hi,
Did you finally figure this out, and write a script for it?
Thanks
Forum: Genomic Resequencing 07-23-2012, 11:09 AM
Replies: 2
Views: 2,488
Posted By nupurgupta
Did you figure this out please?

Did you figure this out please?
Forum: Bioinformatics 07-20-2012, 01:47 PM
Replies: 0
Views: 1,032
Posted By nupurgupta
VCF location in consensus sequence

Hi,
I have a VCF file created by running GATK on read files against a reference genome. The variants in the VCF file have 'locations', these are the locations on the reference genome. I also have a...
Forum: Bioinformatics 06-14-2012, 07:06 AM
Replies: 1
Views: 2,086
Posted By nupurgupta
Creating subset BLAST database

I was getting the wrong GI file. Solved
Forum: Bioinformatics 06-14-2012, 06:43 AM
Replies: 3
Views: 11,272
Posted By nupurgupta
Hi, I was wondering if you found a solution for...

Hi,
I was wondering if you found a solution for this? I have been having all kinds of problems creating subset blast databases.
Thanks
Forum: Bioinformatics 06-12-2012, 09:45 AM
Replies: 0
Views: 1,941
Posted By nupurgupta
Error running blastdbaliastool

SOLVED: The makedb tool was not creating index files. I directly downloaded the database from NCBI and it is working.

Hi,
I am running command line blastplus, and need to blast against bacteria....
Forum: Bioinformatics 06-08-2012, 08:53 AM
Replies: 6
Views: 1,860
Posted By nupurgupta
Yes, you are right! Sorry I am a newbie to this....

Yes, you are right! Sorry I am a newbie to this. Have found a bacterial database

ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Archaea_Bacteria/

Am going to get it now.
Forum: Bioinformatics 06-08-2012, 08:18 AM
Replies: 6
Views: 1,860
Posted By nupurgupta
I was using NCBI blast on microbial data. ...

I was using NCBI blast on microbial data.
http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi
Forum: Bioinformatics 06-08-2012, 08:16 AM
Replies: 7
Views: 3,697
Posted By nupurgupta
OK...no I need to do it against the microbial...

OK...no I need to do it against the microbial database. I need to run BLAST on my local machine from the command line. Setting up an automation pipeline. Unfortunately I have proxy issues connecting...
Forum: Bioinformatics 06-08-2012, 07:08 AM
Replies: 6
Views: 1,860
Posted By nupurgupta
Thanks for the perspective. But I downloaded the...

Thanks for the perspective. But I downloaded the microbial database from ncbi. ftp://ftp.ncbi.nlm.nih.gov/blast/db/16SMicrobial.tar.gz
. I assumed that was the entire microbial database that online...
Forum: Bioinformatics 06-08-2012, 06:58 AM
Replies: 7
Views: 3,697
Posted By nupurgupta
Thank you sooo much. Well, I do need to identify...

Thank you sooo much. Well, I do need to identify the genes in certain parts of the bacterial genomes, so I will go find a fasta file!
Thanks again
Forum: Bioinformatics 06-08-2012, 06:46 AM
Replies: 7
Views: 3,697
Posted By nupurgupta
Thank you so much! I just figured it out. But...

Thank you so much! I just figured it out. But where do I get a protein database from? I'm assuming 16SMicrobial.pal and the like?
Thanks so much
Forum: Bioinformatics 06-08-2012, 06:10 AM
Replies: 6
Views: 1,860
Posted By nupurgupta
BLAST+ strange results

I am running command line blastn with a local copy of a microbial database. My command looks like

blastn -query query.txt -db 16SMicrobial -out newres.txt -wordsize 11 -evalue 10 -gapextend 2...
Forum: Bioinformatics 06-08-2012, 06:08 AM
Replies: 7
Views: 3,697
Posted By nupurgupta
BLAST+ database error

There are posts on topics similar to this - but none that exactly address this issue

I have installed BLAST+ on my Linux machine along with a local copy of the microbial database. "blastn" works...
Forum: Bioinformatics 05-18-2012, 07:47 AM
Replies: 2
Views: 5,198
Posted By nupurgupta
It is a proxy error, I think. I was wondering if...

It is a proxy error, I think. I was wondering if there is a proxy option in blastn itself. I can run it from the browser. But I can also run it directly from applications like clcBio. So the...
Forum: Bioinformatics 05-17-2012, 07:35 AM
Replies: 2
Views: 5,198
Posted By nupurgupta
Command line blast with remote option

Hello,
I am trying to run blastn from my command line with the -remote option, and I get a proxy error as

Error: (311.26) SOCK#1000[6]@130.14.29.110:80: [SOCK::Connect] Failed pending connect():...
Forum: Bioinformatics 04-30-2012, 03:33 PM
Replies: 4
Views: 4,010
Posted By nupurgupta
Hi, Actually I did figure something out for...

Hi,
Actually I did figure something out for this one - see...
Forum: Bioinformatics 04-30-2012, 06:43 AM
Replies: 3
Views: 3,427
Posted By nupurgupta
Thanks very much for this!

Thanks very much for this!
Forum: Bioinformatics 04-27-2012, 07:23 PM
Replies: 3
Views: 3,427
Posted By nupurgupta
SAM flag forward/reverse first/second

Hello,
I am a little confused with the interpretation of SAM flags
From http://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/

...
00010 16 strand of the query (0 for...
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