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Forum: Bioinformatics 08-29-2013, 08:23 AM
Replies: 4
Views: 4,325
Posted By niti217
Thanks again so much. I am excited, can't wait to...

Thanks again so much. I am excited, can't wait to see the results.
Forum: Bioinformatics 08-28-2013, 10:28 AM
Replies: 4
Views: 4,325
Posted By niti217
Thanks so much for the useful input. Though I...

Thanks so much for the useful input. Though I have one more question - to blastx against a protein db, is there an automated way to do for 1800 + genes.

thanks again for your time on this.
Forum: Bioinformatics 08-28-2013, 08:57 AM
Replies: 25
Views: 20,286
Posted By niti217
I was wondering if I could use GFF-Ex to seek...

I was wondering if I could use GFF-Ex to seek information on the reverse strand - especially the non coding regions on the opposite strand. Please let me know. Thanks
Forum: Bioinformatics 08-28-2013, 08:25 AM
Replies: 4
Views: 4,325
Posted By niti217
BLAST - plus/minus strand - non coding region information

Hi

First of all thanks for looking into my post. I need to seek information about non protein coding regions in the reverse strand, using either BLAST or any other tools.

For example if I have...
Forum: RNA Sequencing 07-18-2013, 11:54 AM
Replies: 0
Views: 1,461
Posted By niti217
Tophat/Cufflinks - Transcripts biotype - protein_coding or ncRNA

Hi

I tried to look online on various forums for this problem, unfortunately could not seek much help.

1. From my cufflinks output, for the various genes, I was trying to find their...
Forum: Bioinformatics 03-14-2012, 08:26 AM
Replies: 2
Views: 1,360
Posted By niti217
Thanks so much for the reply. I am sorry that I...

Thanks so much for the reply.
I am sorry that I didn't mention it right. Yes I am indeed looking for the antisense strands.

Thanks again, I will look into Ensembl's biomart.
Forum: Bioinformatics 03-12-2012, 08:13 AM
Replies: 2
Views: 1,360
Posted By niti217
antisense transcripts for all genes in signalling pathway

Hi
I was wondering if its possible to find sense-antisense strands for all the genes involved in a particular signaling pathway.
When I use UCSC genome browser, it only lets me enter a gene name...
Forum: Bioinformatics 01-03-2012, 09:13 AM
Replies: 10
Views: 5,391
Posted By niti217
Thanks so much for your help. I really appreciate...

Thanks so much for your help. I really appreciate it.
Forum: Bioinformatics 12-28-2011, 11:07 AM
Replies: 10
Views: 5,391
Posted By niti217
I am having similar problem - any help would be...

I am having similar problem - any help would be greatly appreciated.

I am trying to index Homo_sapiens.GRCh37 ...fa file using the command

bwa index -p myGenome -a bwtsw /directory/myGenome.fa...
Forum: Bioinformatics 12-22-2011, 10:46 AM
Replies: 29
Views: 16,994
Posted By niti217
I am having similar problem - past 5 hours i...

I am having similar problem - past 5 hours i spent on debugging error -but in vain.
I would really appreciate any help in this regard.

I am trying to index Homo_sapiens.GRCh37 ...fa file using...
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