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Forum: Bioinformatics 11-05-2013, 03:55 AM
Replies: 9
Views: 3,997
Posted By zhidkov.ilia
Hi, you can change your alignment format output...

Hi,
you can change your alignment format output :

emboss/bin/water seq1 seq2 -gapopen 10.0 -gapextend 0.5 -aformat score -outfile aln.tab

Output will show only the names of the...
Forum: Bioinformatics 10-22-2013, 02:59 AM
Replies: 10
Views: 2,634
Posted By zhidkov.ilia
Sounds like question to PerlMonks forum, you can...

Sounds like question to PerlMonks forum, you can ask there how properly use 'substr' function for your tasks.
Forum: Bioinformatics 03-06-2013, 06:32 AM
Replies: 5
Views: 1,495
Posted By zhidkov.ilia
Does "ref_genome.fasta" indexed?

Does "ref_genome.fasta" indexed?
Forum: Bioinformatics 02-25-2013, 06:34 AM
Replies: 17
Views: 33,076
Posted By zhidkov.ilia
Get best alignment of blast results (based on bit...

Get best alignment of blast results (based on bit score):
blastn -query your.fa -db your_db.fa -outfmt 6 | sort -k1,1 -k12,12nr -k11,11n | sort -u -k1,1 --merge > best_single_hits.blastn

This...
Forum: General 09-02-2012, 08:39 AM
Replies: 3
Views: 2,507
Posted By zhidkov.ilia
You can start with literature review (look for...

You can start with literature review (look for papers of plant genomes de-novo assembly and what strategies were used). There is a review by McCombie WR et al (PMID: 22546054), which might be useful...
Forum: Bioinformatics 09-02-2012, 08:25 AM
Replies: 1
Views: 2,373
Posted By zhidkov.ilia
Some genes transcribed from opposite strand of...

Some genes transcribed from opposite strand of DNA, resulting in reverse coordinates. You can add additional column (i.e. strand) adding '+' in cases when start_position < end_position and '-'...
Forum: RNA Sequencing 03-07-2012, 06:13 AM
Replies: 5
Views: 2,095
Posted By zhidkov.ilia
This was modified from Aaaron Quinlan approach...

This was modified from Aaaron Quinlan approach (http://biostar.stackexchange.com/questions/6567/selecting-random-pairs-from-fastq):
awk 'BEGIN{srand()}; {OFS="\t";getline seqs; getline sep; getline...
Forum: RNA Sequencing 03-07-2012, 03:44 AM
Replies: 5
Views: 2,095
Posted By zhidkov.ilia
One of many options is to use Galaxy...

One of many options is to use Galaxy (http://main.g2.bx.psu.edu/): turn your fastq file to tabular and replace the dots with 'N' in second column, then convert the table back to fastq.
(You can look...
Forum: General 09-22-2011, 06:48 AM
Replies: 5
Views: 2,313
Posted By zhidkov.ilia
Let me rephrase my last comment: If duplicated...

Let me rephrase my last comment:
If duplicated reads don't contribute to downstream the de novo assembly pipe, it will be good idea to remove them.

Ilia
Forum: General 09-21-2011, 01:28 AM
Replies: 5
Views: 2,313
Posted By zhidkov.ilia
So when you assemble reads in to contigs, you...

So when you assemble reads in to contigs, you will prefer that at least several reads will support the assembly. If you will have identical reads, you might obtain false contigs.

Ilia
Forum: General 09-21-2011, 12:21 AM
Replies: 5
Views: 2,313
Posted By zhidkov.ilia
I think duplicated reads removed to avoid biases...

I think duplicated reads removed to avoid biases that resulted from library preparation (for example) and not for reduction of data for de-novo assembly.

Ilia
Forum: Bioinformatics 09-07-2011, 02:58 AM
Replies: 11
Views: 31,844
Posted By zhidkov.ilia
The right approach (most probably) will be to use...

The right approach (most probably) will be to use blastx.
(taken from NCBI - tblastx takes a nucleotide query sequence, translates it in all six frames, and compares those translations to the...
Forum: Bioinformatics 07-24-2011, 01:14 AM
Replies: 3
Views: 4,285
Posted By zhidkov.ilia
Hi ojy, you can try use Sequencher...

Hi ojy,
you can try use Sequencher (http://genecodes.com/?referrer=20years&gclid=CICtt-PCmaoCFYdH3godv0BYyQ), in this case you will have mapping and visualization (use the demo version see if it...
Forum: Bioinformatics 07-02-2011, 04:35 AM
Replies: 3
Views: 1,852
Posted By zhidkov.ilia
Hi semma, your question fits better to...

Hi semma,
your question fits better to PerlMonks:
http://www.perlmonks.org/

Can you give an example of expected INPUT and expected OUTPUT, it might help to figure out where is your bug in...
Forum: Bioinformatics 06-28-2011, 06:14 AM
Replies: 2
Views: 1,906
Posted By zhidkov.ilia
Hi rubyb, you can generate pileup file from...

Hi rubyb,
you can generate pileup file from sam/bam file and then look for not continuous numbers correspond to positions in reference sequence. For example:
chr1 333 A 10 …..,,,,, IIIII...
Forum: Bioinformatics 06-27-2011, 09:30 AM
Replies: 3
Views: 3,820
Posted By zhidkov.ilia
Regarding the error message you got, there is...

Regarding the error message you got, there is some discussion at:http://seqanswers.com/forums/showthread.php?t=3551
If you moving out the reads (from sam file) corresponding to rRNA, you can remove...
Forum: Bioinformatics 06-27-2011, 08:23 AM
Replies: 3
Views: 3,820
Posted By zhidkov.ilia
How did you removed the reads from SAM which...

How did you removed the reads from SAM which correspond to rRNA?
Forum: Bioinformatics 02-17-2011, 06:53 AM
Replies: 27
Views: 30,109
Posted By zhidkov.ilia
After all changes in Make file were done and you...

After all changes in Make file were done and you run make command, type ./samtools.exe to run the samtools
Forum: Bioinformatics 01-19-2011, 12:21 PM
Replies: 5
Views: 2,506
Posted By zhidkov.ilia
Ok, found this: ...

Ok, found this:
http://seqanswers.com/forums/showthread.php?t=7488

think it has the answer you looked for

PS
Learned something new myself, thank you
Forum: Bioinformatics 01-19-2011, 11:55 AM
Replies: 5
Views: 2,506
Posted By zhidkov.ilia
--trim option suppose to be 0 by default...

--trim option suppose to be 0 by default...
Forum: Bioinformatics 01-19-2011, 10:57 AM
Replies: 5
Views: 2,506
Posted By zhidkov.ilia
Hi SongLi, one of the options in bowtie is...

Hi SongLi,
one of the options in bowtie is trimimng bases from:
" -5/--trim5 <int>
Trim <int> bases from high-quality (left) end of each read before alignment (default: 0).

-3/--trim3 <int>
...
Forum: Bioinformatics 01-16-2011, 01:31 AM
Replies: 3
Views: 8,022
Posted By zhidkov.ilia
Hi whfwind, I think your question was asked...

Hi whfwind,
I think your question was asked before:



Ilia
Forum: Bioinformatics 01-13-2011, 10:53 AM
Replies: 6
Views: 8,927
Posted By zhidkov.ilia
Hope this will help: ...

Hope this will help:

http://seqanswers.com/forums/showthread.php?t=8653
Forum: Bioinformatics 01-09-2011, 06:32 AM
Replies: 9
Views: 6,612
Posted By zhidkov.ilia
Hi harrike, I'll try to give you short answer...

Hi harrike,
I'll try to give you short answer to your vey long question.
You should use the qual files in order to perform more reliable alignment (the quality of base will help you to decrease...
Forum: Introductions 12-02-2010, 02:43 AM
Replies: 0
Views: 996
Posted By zhidkov.ilia
Smile Hello

Hello to NextGenSeq community
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