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Forum: De novo discovery 11-20-2013, 03:43 AM
Replies: 2
Views: 1,526
Posted By rahularjun86
Does velvet generate different assemblies from the same input data and same velvet pa

Hi all,

I am using four different libraries of read size 76bps, insert sizes are 300bps, 1kb, 8kb and 12kb. Expected genome size is 80MB.

I am running velvet using these four libraries....
Forum: De novo discovery 10-20-2013, 12:04 PM
Replies: 0
Views: 1,179
Posted By rahularjun86
Does velvet assembler use RAM of all nodes altogether?

Dear All,

I have been doing an assembly using four lanes of Illumina Hiseq. I have 300bps, 800bps, 8kb and 20Kb insert libraries. Genome size is 80 MB and genome coverage of reads is more than...
Forum: Illumina/Solexa 01-15-2013, 05:17 AM
Replies: 6
Views: 1,471
Posted By rahularjun86
Hi, You can look here:...

Hi,
You can look here: http://intron.ccam.uchc.edu/groups/tgcore/wiki/013c0/Solexa_Library_Primer_Sequences.html
unix grep command can be used for rough idea of adapters and primers in your...
Forum: Bioinformatics 11-03-2012, 04:52 PM
Replies: 0
Views: 1,012
Posted By rahularjun86
Question codeml fix_omega and omega

HI,
I am using codeml in my analysis. The use of "fix_omega and omega" parameters of codeml.ctl file is not clear to me. It would be great if someone could explain the use of these parameters. ...
Forum: Bioinformatics 10-26-2012, 02:06 AM
Replies: 3
Views: 2,069
Posted By rahularjun86
Hi Lisanne, Have you created the index of...

Hi Lisanne,
Have you created the index of reference genome with bowtie2-build? and try to run bowtie with example data (/bowtie2-2.0.0-beta3/example).

Try following commands:

bowtie2-build...
Forum: Bioinformatics 10-22-2012, 08:31 AM
Replies: 3
Views: 3,315
Posted By rahularjun86
Hi, This could be of your interest...

Hi,
This could be of your interest http://seqanswers.com/forums/showthread.php?t=4301&highlight=Ray.
Thanks,
Rahul
Forum: Bioinformatics 10-22-2012, 07:49 AM
Replies: 0
Views: 673
Posted By rahularjun86
Question Defining new gene Clusters

Hi,
I am interested in defining gene clusters(Gene having same functions/protein products) in a nematode genome. Is there any available software/methods defining these clusters? I have gone through...
Forum: Bioinformatics 10-15-2012, 04:51 AM
Replies: 7
Views: 1,524
Posted By rahularjun86
Oops sorry, Please use the following command, It...

Oops sorry, Please use the following command, It would consider the word boundaries and will generate accurate results:

Thnx
Forum: Bioinformatics 10-15-2012, 04:46 AM
Replies: 7
Views: 1,524
Posted By rahularjun86
Ok thanks, Please try the following unix one...

Ok thanks, Please try the following unix one liner:

Best,
Rahul
Forum: Bioinformatics 10-15-2012, 04:10 AM
Replies: 7
Views: 1,524
Posted By rahularjun86
You mean where the column1(Gene_Horn) and...

You mean where the column1(Gene_Horn) and column3(Gene_DEGSeq) are same, print the column1, column2 and column3?
Forum: Bioinformatics 10-15-2012, 02:30 AM
Replies: 7
Views: 1,524
Posted By rahularjun86
Hi, You can use unix 'join' command for this...

Hi,
You can use unix 'join' command for this task. Please paste first 5 lines of your input/output files, So that one could write the script. You may refer this link:...
Forum: Bioinformatics 10-15-2012, 02:23 AM
Replies: 9
Views: 1,504
Posted By rahularjun86
Hi, Ya you can concatenate the files, but not...

Hi,
Ya you can concatenate the files, but not reads. Please check the Id's in all of your files,
they should be unique before "cat" command.
You may also consider some data preprocessing...
Forum: Bioinformatics 10-14-2012, 05:28 AM
Replies: 9
Views: 1,504
Posted By rahularjun86
Distance in between (1)------> <-------(2) is...

Distance in between (1)------> <-------(2) is called insert size.
Forum: Bioinformatics 10-14-2012, 05:24 AM
Replies: 9
Views: 1,504
Posted By rahularjun86
Yes, there is no need to concatenate the read...

Yes, there is no need to concatenate the read files, you will lose the pair information. And many of the reads will not map, as they will have insert in-between. Look at the following example:

...
Forum: Bioinformatics 10-14-2012, 04:51 AM
Replies: 9
Views: 1,504
Posted By rahularjun86
Hi dear, The data you have is the paired end...

Hi dear,
The data you have is the paired end data, with read 1 and read 2 fastq files are the short read data files with some insert size, most of the times it is 200-400 bps. Ask for the insert...
Forum: Bioinformatics 09-29-2012, 12:16 PM
Replies: 40
Views: 18,485
Posted By rahularjun86
Hi tnguyen, sorry for replying late. Genome was...

Hi tnguyen,
sorry for replying late. Genome was of ~20Mb and other one was in Gb's. Actually I ran on the cluster and I did'nt check the memory it used.
Best wishes,
Rahul
Forum: Bioinformatics 09-26-2012, 11:24 AM
Replies: 2
Views: 1,027
Posted By rahularjun86
Dear Pinal, What command/parameters have you...

Dear Pinal,
What command/parameters have you used for the assembly? what data do you have single or paired end? what is the Insert size if it is paired end? Have you trimmed the low quality reads?...
Forum: Bioinformatics 09-26-2012, 03:44 AM
Replies: 7
Views: 4,800
Posted By rahularjun86
Dear acyrocks, Please run the attached code...

Dear acyrocks,
Please run the attached code using following command(unix):
perl for_seqanswer_fasta_formatter.pl file1.fasta file2.fasta out.fasta
It is working fine here :)
Best wishes,
Rahul
Forum: Bioinformatics 09-20-2012, 06:37 AM
Replies: 6
Views: 4,947
Posted By rahularjun86
Hi all, Many thanks for your valuable comments....

Hi all,
Many thanks for your valuable comments. :)
Regards,
Rahul
Forum: Bioinformatics 09-10-2012, 10:39 AM
Replies: 6
Views: 4,947
Posted By rahularjun86
Genome synteny plotter

Hi all,
With four sequenced genomes, I want to generate the publishable graphics for the syntenic regions. I could not find the software used in this article...
Forum: General 05-31-2012, 01:53 AM
Replies: 1
Views: 1,280
Posted By rahularjun86
Hi, I used Augustus, Glimmer and Genemark for...

Hi,
I used Augustus, Glimmer and Genemark for gene prediction and then Evigan for consensus gene structures.
Cheers,
Rahul
Forum: Bioinformatics 05-28-2012, 06:16 AM
Replies: 14
Views: 4,372
Posted By rahularjun86
Hi, Have you tried RepeatScout...

Hi,
Have you tried RepeatScout (http://bix.ucsd.edu/repeatscout/). It uses repeatmasker in one of its 6 steps. I used it and got nice results.
Best wishes,
Rahul
Forum: Bioinformatics 05-28-2012, 06:07 AM
Replies: 2
Views: 1,606
Posted By rahularjun86
Hi, 1). Shuffle script is to convert two paired...

Hi,
1). Shuffle script is to convert two paired files to single file readable by velveth. Please go through this link: http://www.molecularevolution.org/resources/activities/velvetbowtie_activity...
Forum: Bioinformatics 05-22-2012, 07:05 AM
Replies: 7
Views: 5,563
Posted By rahularjun86
Hi All, I am also getting an error in the 4th...

Hi All,
I am also getting an error in the 4th Step "orthomclInstallSchema"

[rsharma@primary my_orthomcl_dir]$ orthomclInstallSchema orthomcl.config.template
DBI...
Forum: Bioinformatics 05-14-2012, 11:32 PM
Replies: 2
Views: 1,387
Posted By rahularjun86
Finally I got a perl script, It will extract the...

Finally I got a perl script, It will extract the exon sequences from Fasta file using gff as input. Its here:...
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