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Search: Posts Made By: aniruddha.otago
Forum: Bioinformatics 06-25-2016, 09:18 PM
Replies: 23
Views: 15,653
Posted By aniruddha.otago
I think I have solved the problem now. For some...

I think I have solved the problem now. For some reason gtf_to_sam tool was missing.
Anyways, for this particular analysis at this stage all I am wanting is to identify differential expression and...
Forum: Bioinformatics 06-25-2016, 04:21 PM
Replies: 23
Views: 15,653
Posted By aniruddha.otago
Hi there, I am running cuffmerge and having...

Hi there,

I am running cuffmerge and having this problem:

My command:
cuffmerge -g /home/aniruddha/GTF_files/Human_genome/GRCh37_build_65/Homo_sapiens.GRCh37.65.gtf -p 10...
Forum: Sample Prep / Library Generation 11-25-2012, 10:45 PM
Replies: 11
Views: 8,779
Posted By aniruddha.otago
Hey Guys, I am aiming to perform RNA-seq...

Hey Guys,

I am aiming to perform RNA-seq from human Neutrophils. I am taking peripheral blood and the enriching for Neutrophils ( Ficoll+ NH4cl and also tried Ficoll+dextran and even tried...
Forum: Sample Prep / Library Generation 07-17-2012, 01:43 PM
Replies: 8
Views: 8,332
Posted By aniruddha.otago
yeah.. I woulnt do non-directional myself.....for...

yeah.. I woulnt do non-directional myself.....for methylation I dont see much advantage of the method.. thanks..
Forum: Sample Prep / Library Generation 07-16-2012, 05:32 PM
Replies: 8
Views: 8,332
Posted By aniruddha.otago
Hi Felix, Just out of interest, If...

Hi Felix,

Just out of interest,

If TruSeq adapters are used , I presume they are going to be directional anyways, as the original adaptors are ligated to OT abd OB strands only.
But one tries...
Forum: Bioinformatics 07-04-2012, 03:21 PM
Replies: 7
Views: 4,664
Posted By aniruddha.otago
I have analysed my NGS data from Illumina.....

I have analysed my NGS data from Illumina.. (RRBS).. I have fragments (chromosome, genomic position etc).. I would like to search whether there is any common SNPs present in my fragments. I mean I...
Forum: Epigenetics 04-20-2012, 01:49 PM
Replies: 35
Views: 13,017
Posted By aniruddha.otago
it is done on a reduced represented genome. so,...

it is done on a reduced represented genome. so, say there is a fragment of 100 bp and 8 reads uniquely mapped to that. mind you each fragment and read has to have a CGG or TGG (MspI site) at the...
Forum: Epigenetics 04-19-2012, 06:28 PM
Replies: 35
Views: 13,017
Posted By aniruddha.otago
Hi rskr, We never really thought of trying...

Hi rskr,

We never really thought of trying to do that. We were attempting
to see the performance with real RRBS data which we did. I'm not
sure that going to the trouble of trying to generate...
Forum: Epigenetics 04-18-2012, 10:42 PM
Replies: 35
Views: 13,017
Posted By aniruddha.otago
Hi Yuanxin, Thanks, we have solved the...

Hi Yuanxin,

Thanks, we have solved the problem and it came up with reasonable percentage of methylation. It was useful for the analysis. Thanks.
Forum: Epigenetics 04-03-2012, 08:07 PM
Replies: 35
Views: 13,017
Posted By aniruddha.otago
yeah when we were performing the analysis the...

yeah when we were performing the analysis the latest version was 1.2 ( release, April, 2011). every program has newer version each week, this analysis was done at that time with latest versions of...
Forum: Bioinformatics 04-03-2012, 12:32 PM
Replies: 40
Views: 62,323
Posted By aniruddha.otago
Hi Guys, Recently we have published a paper...

Hi Guys,

Recently we have published a paper in Nucleic Acids research on DNA methylation analysis- "Comparison of alignment software for genome-wide bisulphite sequence data". you might find it...
Forum: Bioinformatics 04-03-2012, 12:31 PM
Replies: 14
Views: 7,856
Posted By aniruddha.otago
Hi Guys, Recently we have published a paper...

Hi Guys,

Recently we have published a paper in Nucleic Acids research on DNA methylation data analysis- "Comparison of alignment software for genome-wide bisulphite sequence data". you might find...
Forum: Epigenetics 04-03-2012, 12:29 PM
Replies: 35
Views: 13,017
Posted By aniruddha.otago
Hi Guys, Recently we have published a paper...

Hi Guys,

Recently we have published a paper in Nucleic Acids research- "Comparison of alignment software for genome-wide bisulphite sequence data". you might find it useful to have a look at it.. ...
Forum: Epigenetics 10-04-2011, 06:47 PM
Replies: 35
Views: 13,017
Posted By aniruddha.otago
Hi simon, We have done some methylation...

Hi simon,

We have done some methylation analysis with RRBS samples (human).. we have compared 3 aligners. (RMAPBS, BSMAP and Bismark) RMAPBS and Bismark came up with reaosanable methylation...
Forum: Illumina/Solexa 05-03-2011, 07:43 PM
Replies: 35
Views: 49,279
Posted By aniruddha.otago
Hi All, I am preparing libraries for...

Hi All,

I am preparing libraries for methylation sequencing using the true-seq kit. I will do bisulphite conversion after size selection. Can anyone tell me the how to get / to design the primers...
Forum: Bioinformatics 09-22-2010, 08:02 PM
Replies: 40
Views: 62,323
Posted By aniruddha.otago
Hi felix, send you an email. Please reply.

Hi felix,

send you an email. Please reply.
Forum: Bioinformatics 09-09-2010, 08:42 PM
Replies: 40
Views: 62,323
Posted By aniruddha.otago
hi is there any feedback on my above query....

hi is there any feedback on my above query....
Forum: Bioinformatics 09-09-2010, 03:41 AM
Replies: 40
Views: 62,323
Posted By aniruddha.otago
I am copying a part of aligned read from BSMAP......

I am copying a part of aligned read from BSMAP... Guys pease help how to interpret the methylation from here...... ur feedbacks will help me to have a clearer understanding of the data..



...
Forum: Bioinformatics 09-09-2010, 03:41 AM
Replies: 40
Views: 62,323
Posted By aniruddha.otago
I am copying a part of aligned read from BSMAP......

I am copying a part of aligned read from BSMAP... Guys pease help how to interpret the methylation from here...... ur feedbacks will help me to have a clearer understanding of the data..
Forum: Bioinformatics 09-09-2010, 03:38 AM
Replies: 40
Views: 62,323
Posted By aniruddha.otago
did anybody used the BS_SEEKER programme ??? it...

did anybody used the BS_SEEKER programme ??? it seems that its faster than BSMAP. I tried to run BSMAP and it really slow. is that normal... anyfeedbacks from the previous users ??
Forum: Epigenetics 02-03-2010, 03:13 AM
Replies: 1
Views: 3,076
Posted By aniruddha.otago
Help with bisulfite sequencing

Hi,
We are daling bisulphite sequencing and have send DNA samples now for sequencing to illumina/solexa. can any one tell me how can i deal with the data after sequencing. my study is on DNA...
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