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Forum: Bioinformatics 07-12-2013, 06:17 AM
Replies: 2
Views: 3,070
Posted By babi2305
Hi, I am using mirDeep2 for miRNA prediction...

Hi,

I am using mirDeep2 for miRNA prediction and its super fast, generating very nice output files. Are you looking for other miRNA prediction tools? I would suggest first you must start with...
Forum: Bioinformatics 05-07-2013, 06:12 AM
Replies: 9
Views: 15,743
Posted By babi2305
Star doubt

Hello Alexander,

I am using STAR for my single-end small RNAseq data (15-46 read length) and its working great. thanks! However, since its new, I can't find much help on public forums, there are...
Forum: Bioinformatics 04-02-2013, 02:17 PM
Replies: 0
Views: 1,249
Posted By babi2305
Lightbulb How to work with biological replicates

Hello everyone,

I am working with small-RNA(~50ntds) cancer samples, RNA-seq data. I have tumors and normal cell samples with biological replicates of each sample. Using bed-tools coverageBed I...
Forum: Bioinformatics 03-05-2013, 05:07 AM
Replies: 1
Views: 1,932
Posted By babi2305
How cuffdiff works?

Greetings everyone!

I am stuck with cuffdiff output. Can anyone please give me an idea about how cuffdiff works? I am more interested in finding novel genes/isoforms. I gave the combined.gtf (from...
Forum: Bioinformatics 03-05-2013, 05:00 AM
Replies: 9
Views: 15,743
Posted By babi2305
How cuffdiff works? Need to know the novel transcripts

Thanks so much, I used the gtf file from gencode v15 and it worked fine. Now I am stuck with cuffdiff output. Can you also give me an idea about how cuffdiff works? I am more interested in finding...
Forum: Bioinformatics 02-26-2013, 07:56 AM
Replies: 9
Views: 15,743
Posted By babi2305
Cufflink producing 0.0 FPKM values for Ensembl matched transcripts

Thanks so much for replying. I couldn't find much reference on poly A+/polyA-..still i have started my work with the analysis of cufflinks output. Now problem is using cufflink '-g' option and giving...
Forum: Bioinformatics 02-21-2013, 11:51 PM
Replies: 9
Views: 15,743
Posted By babi2305
Thankyou alexdobin. It is much help. I am just in...

Thankyou alexdobin. It is much help. I am just in starting phase right now.By the way I also need to compare between ployA+ and poly A- RNA-seq data of cytosol and nucleus(A+/A-) taken from encode,...
Forum: Bioinformatics 02-20-2013, 07:10 AM
Replies: 9
Views: 15,743
Posted By babi2305
STAR-alignment/confusion with mismatches & multi-mapping parameter

Hello everyone,


1. I used STAR for mapping RNA seq data with default parameters only changing --outFilterMismatchNmax 5 (allowing 5 mismatches, default was 10). I am now confused if I should...
Forum: Bioinformatics 02-13-2013, 11:50 AM
Replies: 0
Views: 1,156
Posted By babi2305
Methodology used by Fastx clipper??

Hello everyone,

Can somebody tell me here the methodology used by Fastx clipper to trim reads? and if possible about cutadapt also..?? I am using FastX clipper to trim single end adapters (at 3')...
Forum: Bioinformatics 02-06-2013, 11:11 AM
Replies: 7
Views: 5,948
Posted By babi2305
Thankyou..I am reading it..will get back :)

Thankyou..I am reading it..will get back :)
Forum: Bioinformatics 02-06-2013, 10:55 AM
Replies: 7
Views: 5,948
Posted By babi2305
Thankyou so much, yes I know the shell scripting,...

Thankyou so much, yes I know the shell scripting, perl, linux blah blah..I have a basic bash script ready for submitting the job. what I do not know is the cluster computing to map NGS reads i.e....
Forum: Bioinformatics 02-06-2013, 07:59 AM
Replies: 7
Views: 5,948
Posted By babi2305
Hello Genomax, I am working on Gencluster....

Hello Genomax,

I am working on Gencluster. there are right now the following computational nodes
node 1-10.
Each node has 24 cores, 96Gb RAM and a local hard drive of 500Gb.

node 11-20

...
Forum: Bioinformatics 02-06-2013, 07:54 AM
Replies: 7
Views: 5,948
Posted By babi2305
I have replied in the next message.........

I have replied in the next message.........
Forum: Bioinformatics 02-06-2013, 07:21 AM
Replies: 7
Views: 5,948
Posted By babi2305
Using Star/ bowtie on cluster

Hello everyone,

I am just starting my project with RNAseq data analysis. I have my sequences in .fastq format. Its trimmed and good quality wise. Now I need to map it using any tool (bowtie/star),...
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