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Search: Posts Made By: donniemarco
Forum: Bioinformatics 08-10-2011, 02:20 PM
Replies: 10
Views: 16,532
Posted By donniemarco
I think its -F 4 option in BWA!!!

I think its -F 4 option in BWA!!!
Forum: Bioinformatics 06-22-2011, 11:06 AM
Replies: 2
Views: 5,188
Posted By donniemarco
Thanks for the reply!!!

Thanks for the reply!!!
Forum: Bioinformatics 06-22-2011, 10:09 AM
Replies: 2
Views: 5,188
Posted By donniemarco
Base Quality values in BAM file

I want to extract base (calls) quality values from BAM file.

I think these base quality value for each position are present in BAM file as there as Recalibration tool from GATK that uses them. ...
Forum: Bioinformatics 06-22-2011, 09:56 AM
Replies: 4
Views: 2,053
Posted By donniemarco
(I would like to obtain the number of A,C,G and T...

(I would like to obtain the number of A,C,G and T at each position of each contig from a SAM/BAM file.)

I think GATK tools does that. I am also using it to calculate the breakdown of each...
Forum: Bioinformatics 08-06-2010, 08:27 AM
Replies: 10
Views: 16,532
Posted By donniemarco
thanks for your reply Aleferna. Its a great help....

thanks for your reply Aleferna. Its a great help. I have cleaned my sequences already.
Forum: Bioinformatics 07-29-2010, 03:25 PM
Replies: 10
Views: 16,532
Posted By donniemarco
bwa minimum map quality

Is there as anything as minimum or optimal mapq in the bwa.

I plan to take unique query sequences with highest mapq but still not able to figure the cutoff to use it for the analysis.

Any help...
Forum: Bioinformatics 07-25-2010, 06:41 PM
Replies: 7
Views: 4,413
Posted By donniemarco
same error

hi everyone, i got the same error:
***************
hi all I m using Mosaik and create jump database with Mosaikjumb command which is successfully create the jump database but after that when i run...
Forum: Bioinformatics 07-21-2010, 01:07 PM
Replies: 6
Views: 2,131
Posted By donniemarco
cat all files

maybe concatting different files might get little tedious. i tried:
cat chr*.fa >> human_ref.fa

it worked well.
Forum: Bioinformatics 07-21-2010, 12:52 PM
Replies: 2
Views: 2,923
Posted By donniemarco
How can I create one single dat example...

How can I create one single dat example total.ref.dat for the entire genome. The data available are in seperate files for each chromosome.
I want to run entire index data with mosaik for all the...
Forum: 454 Pyrosequencing 01-22-2010, 12:31 PM
Replies: 29
Views: 14,514
Posted By donniemarco
Thanks, I looked into the error file and it seems...

Thanks, I looked into the error file and it seems to have run out of memory.

"************
Ran out of memory: 10911460019 bytes requested.
Error! cap3 failure detected (code=256) on: CL1...
Forum: 454 Pyrosequencing 01-22-2010, 08:37 AM
Replies: 29
Views: 14,514
Posted By donniemarco
yes, i got the same error and i downloaded the...

yes, i got the same error and i downloaded the cap3 specific to my machine as suggested by Sklages.
It seemed to have worked as it didn't gave the same error message about cap3 but crashed after...
Forum: 454 Pyrosequencing 01-21-2010, 02:58 PM
Replies: 29
Views: 14,514
Posted By donniemarco
Thanks for the reply. I will run assembling...

Thanks for the reply.

I will run assembling with mira and see how it goes. BTW, earlier I ran the same data with TIGR but it seems to have crashed while performing assembling with CAP3 (it...
Forum: 454 Pyrosequencing 01-20-2010, 09:08 AM
Replies: 29
Views: 14,514
Posted By donniemarco
Hi Sven, Thanks for your helpful reply. ...

Hi Sven,

Thanks for your helpful reply.

If I extract all the cluster forming sequences say 213, 161 and 406 (actual sequence 214, 162, 407: thanks for pointing this as I had missed this) from...
Forum: 454 Pyrosequencing 01-18-2010, 05:18 PM
Replies: 29
Views: 14,514
Posted By donniemarco
Wcd

I am trying to run WCD however I am not able to generate sequence cluster that is generated by WCD with default parameters as follows:
wcd -c -N 4 -o test.clust -g -t testSeq.fna


I get the...
Forum: 454 Pyrosequencing 10-19-2009, 08:55 AM
Replies: 3
Views: 5,099
Posted By donniemarco
Thanks for your reply. It was really helpful. ...

Thanks for your reply. It was really helpful.

What about PolyA and PolyT sequences? How long any sub-sequence be to qualify as polyA or polyT.
Forum: 454 Pyrosequencing 10-16-2009, 12:26 PM
Replies: 3
Views: 5,099
Posted By donniemarco
non paired adapters in 454 data

Can anyone please let me know any preprocessing steps (like cleansing adapters or any other steps) for non paired 454 sequenced data and any available tool that allows the same, before assembling is...
Forum: 454 Pyrosequencing 08-15-2009, 06:53 PM
Replies: 2
Views: 3,134
Posted By donniemarco
454 assembling against reference genome

Hi,
Can anyone please let me know from where I can download "Reference Sequence" that I can run against BLAT. I came across this term quite too frequently but I am unsure which file might be the...
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