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Old 04-17-2013, 03:44 AM   #1
Location: Italy

Join Date: Aug 2012
Posts: 27
Post I would like to know basic pipeline for analysis of miRNA from SOLID seq data ?

We have raw data in COLOR space format (.csfasta) and would like to profile and analyze it in order to find known and novel miRNA in sample. Further we are also looking for Diff. expression between two samples.
Any suggestion ???
Actually i am facing problem to handle directly from .csfasta because as per my survey, i know many tools (web serivces/offline tool ) but No one or very few able to handle .csfasta file for analysis of mapping,known,novel and diff exp.

Thanks & looking forward for your valuable input.
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Old 04-18-2013, 08:57 PM   #2
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abi had their own tool called RNA2MAP.
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Old 04-22-2013, 09:40 AM   #3
Milan Radovich
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Use Life Tech's LifeScope 2.5 and that will get you the mapping and the count data that you need for subsequent differential expression analysis
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Old 05-13-2013, 09:52 PM   #4
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Originally Posted by unique379 View Post
to do so...i got fastq output in decode format cs2bs (without 5' primer T and 3' adapter)...

Now i am trying to align this fastq output with Bowtie with this command line arguments..(what i got from here:

bowtie --sam -q -a -n 0 -l 15 -e 99999 -k 200 --chunkmbs 1024 --best...

But i am not sure that i am in right way.....??

could someone suggest me to align this fastq with right option of bowtie in order to get best alignment ?? or is that correct arguments ??
Hi Unique379,

I am confused with your comment regarding getting fastq format in decode format? There are some serious conversion issues if one directly converts color space to base space. Much better if you leave everything in color space, and this means you will have to index the reference in colorspace (using the -C parameter in bowtie-build).

Did you know you can use bowtie to map with existing csfasta + qual data files? Here is an example of a command line we have previously used:

bowtie -C -f --integer-quals -l 21 -n 1 --nomaqround --chunkmbs 256 --best --col-cqual --col-keepends --sam --quals input.qual bowtie_ref_index input.csfasta output.sam

You (and others) might be interested in a new software tool I have developed to help analyse miRNA data. Visit for detailed information. The website describes the miRspring document as well as providing some basic information on preparing BAM files.

Good luck! Would be interested to hear your findings when comparing to lifescope output.

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bioinformatics sequencing, mirna-seq, ngs data analysis, solid 5500, solid p2 adapter

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