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Forum: Bioinformatics 03-20-2014, 12:20 AM
Replies: 189
Views: 83,752
Posted By bharat_iyengar
Is it possible to alter the minimum seed length...

Is it possible to alter the minimum seed length in trimmomatic.SE, for adapter clipping ?

If it is not explicit which one of the source files has to be edited ?
Forum: Bioinformatics 03-03-2014, 05:57 AM
Replies: 2
Views: 1,314
Posted By bharat_iyengar
Even with targetscan you can build your own...

Even with targetscan you can build your own families.. It is pretty cumbersome. It is not straightforward. With miRanda you can do a fasta vs fasta prediction and it is fairly simple. You can add...
Forum: Bioinformatics 03-03-2014, 04:37 AM
Replies: 2
Views: 2,283
Posted By bharat_iyengar
IO redirection in trimmomatic

Is it possible to pipe inputs to trimmomatic. Similarly can I redirect the output to stdout ?
Forum: Bioinformatics 04-21-2013, 07:26 PM
Replies: 11
Views: 10,601
Posted By bharat_iyengar
Easiest thing to do would be to get the...

Easiest thing to do would be to get the executables directly. Boost 1.52 has some problem linking with cufflinks.
Forum: Bioinformatics 03-20-2013, 11:22 PM
Replies: 0
Views: 1,509
Posted By bharat_iyengar
Drosophila Refseq

NCBI Refseq FTP doesn't have Drosophila sequences.
The problem with Flybase is that there is no single non-redundant database file for the entire transcriptome, but it has individual files for...
Forum: Bioinformatics 02-26-2013, 01:13 AM
Replies: 4
Views: 4,360
Posted By bharat_iyengar
i am facing a similar problem.. I was...

i am facing a similar problem..

I was interested in getting some information from a publicly available hiseq2000 small RNA seq data from drosophila.
However, the library was prepared by cloning...
Forum: Bioinformatics 01-18-2013, 01:38 AM
Replies: 0
Views: 1,926
Posted By bharat_iyengar
Cufflinks statistical model

I needed a little help in understanding the abundance estimation by
Cufflinks.
Please refer to cufflinks supplementary methods.

Let me reiterate some of the key points/definitions; for the sake...
Forum: RNA Sequencing 01-17-2013, 09:43 PM
Replies: 23
Views: 10,704
Posted By bharat_iyengar
I had been doing fair amount of RNAseq and small...

I had been doing fair amount of RNAseq and small RNAseq analysis but I still have a basic doubt regarding small RNAseq.

for RNAs smaller than the typical read length, where do the extra bases come...
Forum: Bioinformatics 12-25-2012, 01:41 AM
Replies: 0
Views: 1,722
Posted By bharat_iyengar
mirdeep2

Anyone using mirdeep2. If yes I shall discuss my problem..
Forum: Bioinformatics 12-25-2012, 01:39 AM
Replies: 2
Views: 2,962
Posted By bharat_iyengar
i think its too late now but the scoring formula...

i think its too late now but the scoring formula is given in mirdeep1 paper in nature biotech
Forum: Bioinformatics 12-23-2012, 03:43 AM
Replies: 7
Views: 4,002
Posted By bharat_iyengar
i got this error while running bowtie (almost...

i got this error while running bowtie (almost near end)

Error while flushing and closing output
terminate called after throwing an instance of 'int'
Aborted (core dumped)

is it because of...
Forum: Bioinformatics 12-22-2012, 10:46 PM
Replies: 16
Views: 7,835
Posted By bharat_iyengar
but its all annotated.. i know what the variants...

but its all annotated.. i know what the variants are..


most of the times the input RNA for seq is poly-A fractionated.
most regulatory/intermediate guys are already lost..

the...
Forum: Bioinformatics 12-22-2012, 09:39 PM
Replies: 16
Views: 7,835
Posted By bharat_iyengar
Understood. But i intend to know the reason why...

Understood. But i intend to know the reason why the consensus has been so?

Why is it logically better to map the reads to genome and provide annotations rather than mapping to an already...
Forum: Bioinformatics 12-22-2012, 05:49 AM
Replies: 16
Views: 7,835
Posted By bharat_iyengar
can I skip Tophat???

I want to quantify Refseq RNA based on RNAseq data and I am using bowtie-tophat-cufflinks algorithm for this. I have a doubt regarding the necessity of tophat.

If I have an index of transcriptome...
Forum: Bioinformatics 12-17-2012, 08:07 AM
Replies: 5
Views: 2,125
Posted By bharat_iyengar
i shall try. thanks :)

i shall try. thanks :)
Forum: Bioinformatics 12-17-2012, 08:02 AM
Replies: 5
Views: 2,125
Posted By bharat_iyengar
I had corrected that particular problem,which was...

I had corrected that particular problem,which was because of improper definition of a variable. But then another one appeared which is perhaps because boost_system library is not linked during...
Forum: Bioinformatics 12-16-2012, 10:26 PM
Replies: 11
Views: 10,601
Posted By bharat_iyengar
I did this but there happens to be one more...

I did this but there happens to be one more error:

make all-recursive
make[1]: Entering directory `/media/sda8/bharat/genomes/cufflinks-2.0.2'
Making all in src
make[2]: Entering directory...
Forum: Bioinformatics 12-16-2012, 09:31 PM
Replies: 5
Views: 2,125
Posted By bharat_iyengar
problem installing cufflinks

there was no problem configuring Cufflinks v2.02 but when i make it i get an error like this

make all-recursive
make[1]: Entering directory `/media/sda8/bharat/genomes/cufflinks-2.0.2'
Making...
Forum: Bioinformatics 12-16-2012, 08:31 PM
Replies: 15
Views: 12,762
Posted By bharat_iyengar
Can samtools be copied to ANY directory in PATH.....

Can samtools be copied to ANY directory in PATH.. i have given default path /usr/local

should i copy satools binary to /usr/local/bin ?
Forum: Bioinformatics 12-13-2012, 09:17 PM
Replies: 2
Views: 1,991
Posted By bharat_iyengar
Quality filtering

I am new to the field but from what I gathered is that it is essential to filter sequences with low quality (phred scores).

But what I generally observed is that I lose ~70-80% reads from some...
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