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Search: Posts Made By: amarth
Forum: Bioinformatics 10-22-2013, 08:43 AM
Replies: 8
Views: 5,416
Posted By amarth
dude, 1. tblastx your query with the...

dude,

1. tblastx your query with the database sequences, and save the output in the standard format. (most important: The ID and frame)
2. retrieve such sequences by ID and make a fasta file.
3....
Forum: Bioinformatics 07-01-2013, 11:42 AM
Replies: 4
Views: 2,893
Posted By amarth
It seems, that is an error after the first error ...

It seems, that is an error after the first error


http://stackoverflow.com/questions/5535548/make-error-1-error

http://forums.fedoraforum.org/showthread.php?t=266446

As far as i understood,...
Forum: Bioinformatics 07-01-2013, 09:29 AM
Replies: 2
Views: 1,285
Posted By amarth
ncRNA from RNAseq...

Dear all,

I have an experiment where I test three different conditions (you know, usual stuff ;) ). Total RNA was extracted and sequenced by RNAseq, later determined gene expression for each...
Forum: Bioinformatics 07-01-2013, 07:51 AM
Replies: 4
Views: 2,893
Posted By amarth
Check this!!: ...

Check this!!:

http://seqanswers.com/forums/showthread.php?t=16637

Offtopic: Cufflinks runs good on windows?
Forum: Bioinformatics 07-01-2013, 07:44 AM
Replies: 3
Views: 3,532
Posted By amarth
Have you tried to convert your BAM file into a...

Have you tried to convert your BAM file into a SAM or Fasta?

Use in the command line:



The SAM file will provide the mapped reads into a specific scaffold. There you can retrieve your reads....
Forum: Bioinformatics 06-28-2013, 12:19 PM
Replies: 15
Views: 19,042
Posted By amarth
Alignment is the comparison between sequences...

Alignment is the comparison between sequences (nucleic acids or aminoacids), the result will be some common letters within their sequence structures.
For example, you have this two sequences of...
Forum: Bioinformatics 06-28-2013, 10:30 AM
Replies: 6
Views: 1,794
Posted By amarth
Smile Cufflinks takes a couples of hours with small...

Cufflinks takes a couples of hours with small samples, I've run 60 millions reads and it takes around 10 hours to complete, I have a Linux Workstation with these specs:

Dual-Core Intel Xeon...
Forum: Bioinformatics 03-05-2013, 07:24 AM
Replies: 1
Views: 1,204
Posted By amarth
Unhappy Issues with Mira

Hi pals


Recently, my objective is to assemble some reads sequenced with Illumina/Solexa in fastq format (around 12 millions reads)...

I've chosen MIRA to make this work, i typed the command:...
Forum: Bioinformatics 03-05-2013, 07:01 AM
Replies: 28
Views: 59,271
Posted By amarth
Smile I second that :)

I second that :)
Forum: Bioinformatics 01-21-2013, 12:15 PM
Replies: 1
Views: 1,103
Posted By amarth
Question Looking for no-hits within Sample & Reference Genome

Hi pals,

This is amarth, and my question is:

How can I extract no-hits data from the alignment of the sample, with the reference genome?


My main goal is not to visualize differential...
Forum: Introductions 01-15-2013, 05:36 AM
Replies: 1
Views: 692
Posted By amarth
quite short, but anyway... íHola amigo! jaja

quite short, but anyway...

íHola amigo! jaja
Forum: Bioinformatics 01-13-2013, 10:19 PM
Replies: 4
Views: 1,490
Posted By amarth
1) Thanks for the advice, :) 2) Could it be...

1) Thanks for the advice, :)

2) Could it be the seq Quality?

http://www.anonmgur.com/up/63a0af02c2905e5678f7c1355c309c54.png

http://www.anonmgur.com/up/6502eebef85fbcbea4769938c880ed61.png
...
Forum: Bioinformatics 01-13-2013, 09:22 PM
Replies: 4
Views: 1,490
Posted By amarth
Question Getting just a few alignments with Tophat2

I made an alignment for a 1.1GB file, the RNA-seq reads were in fastq (Illumina) format. The reference was in fasta, so i decided to convert the large file to fasta... :rolleyes:

Later i made the...
Forum: Introductions 01-13-2013, 08:17 PM
Replies: 0
Views: 850
Posted By amarth
Smile Greetings from a Msc student, Mexico

Hello Seq-pals!

I'm a Msc Student, working on Cinvestav, Mexico... My research involves many stuff related to Bioinformatics (or as I can say, my 2nd Hobbie [1st one's Guitar]).

Despite being...
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