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Search: Posts Made By: Chandana
Forum: Illumina/Solexa 12-17-2012, 07:21 AM
Replies: 3
Views: 1,197
Posted By Chandana
Thanks GenoMax, I have attached the "official"...

Thanks GenoMax, I have attached the "official" reply from the NCBI for my question

"Dear Colleague,

There appears to be no sequence length filter for SRA search. You may try to search the SRA...
Forum: Illumina/Solexa 12-14-2012, 09:42 AM
Replies: 3
Views: 1,197
Posted By Chandana
Locating file in SRA

I wanted to locate some illumina sequencing data for humans of size 130bp and 150bp from the SRA. However, searching with keywords like "Illumina" "130bp" "Human" etc. does not give any results or...
Forum: Illumina/Solexa 04-07-2012, 12:35 PM
Replies: 2
Views: 1,605
Posted By Chandana
Thanks a lot twaddlac, I have solved my problem...

Thanks a lot twaddlac, I have solved my problem using the SRA toolkit.
For splitting SRA fastq to .qual and .csfasta I used the abi-dump tool in SRA toolkit. The script solid2fastq.pl in BWA fails...
Forum: Illumina/Solexa 04-06-2012, 11:25 AM
Replies: 2
Views: 1,605
Posted By Chandana
SOLiD to NCBI SRA

Hi,
Can anyone help me to convert SOLiD data in .qual and .csfasta format into the FASTQ format used by NCBI SRA? Similaly, is there a way to separate a color space FASTQ in NCBI SRA into...
Forum: Bioinformatics 01-11-2012, 10:03 AM
Replies: 0
Views: 1,357
Posted By Chandana
BWA:getting hits with given number of mismatches and indels

Hi,
is it possible to setup BWA to get hits with at most x mismatches and y indels? Although -n x -o 1 -e y would allow x mismatches and y consecutive indels, what if I want to permit non...
Forum: Bioinformatics 12-09-2010, 11:26 PM
Replies: 0
Views: 1,481
Posted By Chandana
BWA:Unique reads in seeding mode

Hi,

When seeding is enabled in BWA, if a read is marked as unique does it mean that the seed portion is uniquely mapped, like in ELAND? or is it that the whole read is uniquely mapped?
Forum: Bioinformatics 12-04-2010, 01:27 AM
Replies: 3
Views: 2,039
Posted By Chandana
Thanks Chipper for the quick reply, but the...

Thanks Chipper for the quick reply, but the script does not seem to work on my case. the reads are like


@ERR012630.16 VAB_solid0029_20100115_QR1000044_50X2_QR10000441_14_61/1...
Forum: Bioinformatics 12-03-2010, 10:53 PM
Replies: 3
Views: 2,039
Posted By Chandana
How to map NCBI SOLiD reads with BWA

Hi,
I have downloaded some SOLiD reads from NCBI and needs to map them using BWA. Should I simply convert 0->A, 1->C etc. or do I need to chop the first two bases in addition?
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