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Search: Posts Made By: naluru
Forum: Vendor Forum 09-14-2011, 11:46 AM
Replies: 1
Views: 3,786
Posted By naluru
I am using CLC Bio Genomics Workbench 4.7.2 to do...

I am using CLC Bio Genomics Workbench 4.7.2 to do smallRNA analysis. Everything works fine and it is very easy to use. However, I am having trouble while looking for novel miRNAs. The user manual do...
Forum: Bioinformatics 04-19-2011, 06:38 AM
Replies: 3
Views: 4,402
Posted By naluru
Thank you for both the suggestions. Thank...

Thank you for both the suggestions.

Thank you, zee. I will try bedTools.

Volks, you are correct and I thought about it. The GFF files in miRBase website have the coordinates only for precursor...
Forum: Bioinformatics 04-19-2011, 05:53 AM
Replies: 3
Views: 4,402
Posted By naluru
miRNA mature and star sequences, isomiRs etc

Hello,

I have asked this question before and didn't get any replies. I thought I will post it again as many others might be having similar problems.

I am working with miRNA-seq data set and I...
Forum: Bioinformatics 03-29-2011, 06:21 AM
Replies: 1
Views: 2,208
Posted By naluru
SAM to blast format

I am also looking for an answer to the above question. If anyone has any ideas, could you please share it.

Thank you.
Forum: Bioinformatics 03-22-2011, 12:39 PM
Replies: 5
Views: 8,358
Posted By naluru
GFF file formatting

Hello,

I downloaded some GFF files from ensembl website and only need a small subset of rows in these files. So, I opened them up in Excel and chose whatever I wanted.

I saved them as tab...
Forum: Bioinformatics 03-22-2011, 12:31 PM
Replies: 132
Views: 55,731
Posted By naluru
Thanks, Marcel. No problem. I will try to work...

Thanks, Marcel. No problem. I will try to work around it.

Neel
Forum: Bioinformatics 03-20-2011, 07:26 AM
Replies: 132
Views: 55,731
Posted By naluru
Thank you, Marcel. It will be really helpful if...

Thank you, Marcel. It will be really helpful if you could provide that code. Do you know how SHRiMP and Mosiak assembler deal with it?

Thank you,
Neel
Forum: Bioinformatics 03-18-2011, 12:37 PM
Replies: 132
Views: 55,731
Posted By naluru
cutadapt - loss of first base in SOLiD reads

Hi Martin,

I am not quite sure if my issue is related to cutadapt but I just thought I will check with you as I used it to trim the adapter.

I used cutadapt to trim the adapter using cutadapt...
Forum: SOLiD 01-13-2011, 07:33 PM
Replies: 1
Views: 2,087
Posted By naluru
Calculating read lengths - SOLiD

I am working with SOLiD data and have trimmed reads. I am trying to calculate the length of the reads and their number. I have seen several publications where they have shown these details.

My...
Forum: Bioinformatics 01-11-2011, 11:11 AM
Replies: 191
Views: 78,534
Posted By naluru
htseq-count for miRNA I am using...

htseq-count for miRNA

I am using "htseq-count" to count the miRNA using their genomic coordinates. It worked very well. But, I am also interested in a more detailed output. I want an output with...
Forum: Bioinformatics 12-28-2010, 11:57 AM
Replies: 20
Views: 18,830
Posted By naluru
samtools tview

Hello,

I am having similar problem as mentioned here earlier. I have a string of N's in the reference genome, when I use the samtools tview command.Only the first 80 bases are present and...
Forum: Bioinformatics 12-27-2010, 07:18 PM
Replies: 132
Views: 55,731
Posted By naluru
cutadapt 0.8

Hi Martin,

I got a chance to use the new version and have couple of questions with regard to the output. I am posting the output below and my questions are in the bottom.

OUTPUT:

Maximum...
Forum: SOLiD 12-11-2010, 08:44 AM
Replies: 5
Views: 5,880
Posted By naluru
Thank you very much for the reply. Exactly thats...

Thank you very much for the reply. Exactly thats how I thought the pipeline should be. But, most of the papers published first align to the genome and then to miRBase. That's what confused me.
...
Forum: SOLiD 12-10-2010, 12:29 PM
Replies: 5
Views: 5,880
Posted By naluru
SmallRNA analysis pipeline

I am little bit confused with the smallRNA analysis pipeline used for analyzing SOLiD results.

Here is what I have read everywhere.

1. Trim the adaptors and convert from csfasta to...
Forum: SOLiD 12-09-2010, 01:08 PM
Replies: 0
Views: 2,456
Posted By naluru
BWA aligner - zebrafish miRNA

Hello,

I have couple of questions with regard to SOLiD reads and BWA aligner for analyzing zebrafish miRNA results.

1. I am using BWA to align my reads and I do not get any unique reads. I am...
Forum: SOLiD 12-09-2010, 09:55 AM
Replies: 0
Views: 2,209
Posted By naluru
csfasta files - miRanalyzer input file format

I am new to NGS and have some SOLiD data. I want to analyze them for miRNA expression. Previously I have used miRanalyzer and DSAP to analyze illumina data. The input file for these web-based tools...
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