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Search: Posts Made By: Joker!sAce
Forum: Bioinformatics 08-25-2011, 04:43 PM
Replies: 0
Views: 1,623
Posted By Joker!sAce
New company in the making. Need team members.

Hi all,

I've set up a system with the intention of commercializing it in a few years. It's supported and guided by teachers at Copenhagen University, Dana Farber Cancer Institute (Harvard) and at...
Forum: Bioinformatics 08-17-2011, 05:44 AM
Replies: 13
Views: 5,958
Posted By Joker!sAce
A size file is just a file with chromosome name...

A size file is just a file with chromosome name and it's length. i've attached 2 text files. The chrom2 is the one you should probably use, the other has lengths of all hg19 chromosomes(alternative...
Forum: Bioinformatics 08-10-2011, 02:10 AM
Replies: 13
Views: 5,958
Posted By Joker!sAce
@ Upendra Thanks a lot for the mail. It all...

@ Upendra

Thanks a lot for the mail. It all works well now.

I have one small question.

In the bed file there are some transcripts with a * instead of +/- for orientation. What does this mean?
Forum: Bioinformatics 08-08-2011, 02:30 AM
Replies: 13
Views: 5,958
Posted By Joker!sAce
Everyone in my department already does. We wanted...

Everyone in my department already does. We wanted to test out scripture. I know that using cufflinks would probably be less challenging given the great documentation.
Forum: Bioinformatics 08-07-2011, 02:49 PM
Replies: 13
Views: 5,958
Posted By Joker!sAce
Hey, That'd be awesome. My e-mail is...

Hey,

That'd be awesome. My e-mail is orsha.pk@gmail.com

I've tried the three versions of scripture they've put on the website, none of them have this older function. Maybe they should include...
Forum: SOLiD 08-07-2011, 04:05 AM
Replies: 5
Views: 4,080
Posted By Joker!sAce
Hi, I looked at this tutorial and was...

Hi,

I looked at this tutorial and was looking for the "scripture_alpha2.jar" file. I cannot find that file anywhere. Any insights or help would be appreciated.

Thanks!
Forum: RNA Sequencing 08-07-2011, 04:03 AM
Replies: 1
Views: 1,588
Posted By Joker!sAce
Hi, I have the same troubles. If you use...

Hi,

I have the same troubles. If you use SAMtools anywhere, your output will be wrong. There are many more unresolved issues too.

I was told that this...
Forum: Bioinformatics 08-07-2011, 04:00 AM
Replies: 1
Views: 1,372
Posted By Joker!sAce
Try using this... perl -ne '@l = split;...

Try using this...

perl -ne '@l = split; $l[4]=1; print "@l[0..11]\n";' < chr1.bed > c.bed

I assume that this file is called chr1.bed.
The output will be stored in c.bed
Forum: Bioinformatics 08-07-2011, 03:38 AM
Replies: 13
Views: 5,958
Posted By Joker!sAce
I was using IGVtools without the genome files....

I was using IGVtools without the genome files. Downloading that, it should hopefully work now. Q2 still stands.
Forum: Bioinformatics 08-07-2011, 03:26 AM
Replies: 13
Views: 5,958
Posted By Joker!sAce
Hi, Thanks for the reply. I have 2...

Hi,

Thanks for the reply.

I have 2 questions on this link...

1. In the IGVtools count command, what is the .genome file? Rather how do you get it? I tried the .fa reference genome but that...
Forum: Bioinformatics 08-06-2011, 07:19 AM
Replies: 13
Views: 5,958
Posted By Joker!sAce
Arrow Transcriptome reconstruction from RNA-seq data using Scripture.

Hi all,

I'm trying to re-construct the transcriptome from RNA-seq data using scripture and I get some errors. I'm pasting a log of errors and commands I've been using.

I have paired end data...
Forum: Bioinformatics 04-11-2011, 04:43 AM
Replies: 11
Views: 11,070
Posted By Joker!sAce
Field MAPQ considers pairing in calculation if...

Field MAPQ considers pairing in calculation if the read is paired. If such a calculation is difficult, 255 is applied, indicating the mapping quality is not available. I assume your query sequences...
Forum: Bioinformatics 04-11-2011, 04:35 AM
Replies: 2
Views: 1,552
Posted By Joker!sAce
I submitted this with a more scientific report...

I submitted this with a more scientific report and I got the highest grade tho :P I'm sure the teachers liked it.

It is useful, it's going to be used in future projects.

Yeah, that's a great...
Forum: Bioinformatics 04-10-2011, 09:44 PM
Replies: 2
Views: 1,552
Posted By Joker!sAce
Need your views on a custom pipeline

Hi,

Here's a link to my most recent presentations. My team created a pipeline to map sequences to a custom dataset using the BWA aligner. The pipeline also gives some stats and does an error...
Forum: Genomic Resequencing 03-16-2011, 04:30 PM
Replies: 7
Views: 5,111
Posted By Joker!sAce
This sequence has been aligned to hg18. I know...

This sequence has been aligned to hg18. I know the chromosomal co-ordinates for hg18 (chr17:7,520,037-7,531,588 - That's the tp53 repressor gene)

How do I proceed from here?
Forum: Genomic Resequencing 03-10-2011, 04:32 AM
Replies: 7
Views: 5,111
Posted By Joker!sAce
My study involves divergence study on the gene...

My study involves divergence study on the gene p53 on short arm of chromosome 17. I need to extract this part of the sequence.

I understand that I can do this in two ways:
1. Get raw fasta reads....
Forum: Genomic Resequencing 02-28-2011, 12:36 PM
Replies: 7
Views: 5,111
Posted By Joker!sAce
I understand that there are a lot of columns in...

I understand that there are a lot of columns in this record.

NA06984-SRR006041.1145152
1040
1
113040605
57
325M
*
0
Forum: Introductions 02-28-2011, 07:31 AM
Replies: 0
Views: 839
Posted By Joker!sAce
Cool Hello!

Hi,

I'm Pranav and I'm from India. I'm doing my Masters in Bio-Informatics at the Copenhagen University in Denmark.

I'm currently working on a pipeline that uses BWA aligner to align an...
Forum: Genomic Resequencing 02-28-2011, 07:20 AM
Replies: 4
Views: 7,980
Posted By Joker!sAce
Hi, I'm working on something similar, almost...

Hi,

I'm working on something similar, almost identical. You could try this script to get all the aligned reads. Pysam can read/ write to SAM files.
Here are two (Documentation 1...
Forum: Introductions 02-28-2011, 07:16 AM
Replies: 33
Views: 9,183
Posted By Joker!sAce
Hey, I'm using IGV too. I'm just starting on it...

Hey, I'm using IGV too. I'm just starting on it and I like it, It's a great tool.
Forum: Genomic Resequencing 02-28-2011, 07:05 AM
Replies: 7
Views: 5,111
Posted By Joker!sAce
Thumbs up Understanding BAM format.

Hi,

I have this output in BAM format.



(This is data from the 1000 genomics project.)

I'm constructing a pipeline to study variations (I get fast-q sequence, index it, align it to ref.seq...
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