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Search: Posts Made By: bi_maniac
Forum: Bioinformatics 05-02-2016, 02:36 PM
Replies: 1
Views: 864
Posted By bi_maniac
http://bmcimmunol.biomedcentral.com/articles/10.11...

http://bmcimmunol.biomedcentral.com/articles/10.1186/s12865-014-0059-7

http://www.genetics.org/content/early/2015/08/21/genetics.115.176735
Forum: General 05-02-2016, 02:10 PM
Replies: 2
Views: 1,096
Posted By bi_maniac
You are right. Excuse me. ...

You are right. Excuse me.

http://bioinformatics.oxfordjournals.org/content/early/2010/11/13/bioinformatics.btq642
http://www.bioinf.uni-leipzig.de/Software/PLEXY/
Forum: General 05-01-2016, 10:36 PM
Replies: 2
Views: 1,096
Posted By bi_maniac
Forum: Bioinformatics 04-23-2016, 08:59 PM
Replies: 1
Views: 864
Posted By bi_maniac
IMonitor and Immunoglobulin Galaxy

Has any of you installed/used one of these software?

IMonitor
Immunoglobulin Galaxy
Forum: General 12-15-2015, 10:40 AM
Replies: 16
Views: 2,647
Posted By bi_maniac
Are command line programs, like samtools that...

Are command line programs, like samtools that difficult to use?

Should lab people study the principles of linux shell?

Should computer people study the principles of biology? To be honest, I...
Forum: General 12-15-2015, 02:01 AM
Replies: 16
Views: 2,647
Posted By bi_maniac
Hi Sylvaint, I assume that in your case...

Hi Sylvaint, I assume that in your case bioinformaticians are like computer consultants. Am I wrong?
Forum: General 12-15-2015, 12:20 AM
Replies: 16
Views: 2,647
Posted By bi_maniac
Cool Laboratory people vs Computer people

Hi people, I do not want to be polemic. I am a newcomer in bioinformatics and just want you to tell me in an open and frank way how are relationships between lab people and computer people in your...
Forum: Bioinformatics 11-15-2015, 12:06 PM
Replies: 5
Views: 2,211
Posted By bi_maniac
^^^^^ It is correctly indented but I do not...

^^^^^
It is correctly indented but I do not know how to leave it well. It did not aloow me to upload it as attachment.
Forum: Bioinformatics 11-15-2015, 11:58 AM
Replies: 5
Views: 2,211
Posted By bi_maniac
I got it. Thank you anyway. from Bio.Data...

I got it. Thank you anyway.

from Bio.Data import IUPACData

#-------------------------------------------
# Functions
#-------------------------------------------

def expand_wildcards(seq):...
Forum: Bioinformatics 11-15-2015, 07:28 AM
Replies: 5
Views: 2,211
Posted By bi_maniac
Can anyone tell me how to expand this ambiguity...

Can anyone tell me how to expand this ambiguity codes with biopython?
I mean, if I call with a sequence like 'YATCG' it returns 2 sequences 'TATCG' and 'CATCG'

Thanks a lot.
Forum: Illumina/Solexa 11-03-2015, 02:34 PM
Replies: 19
Views: 3,022
Posted By bi_maniac
I assume that primer sites are not involved in...

I assume that primer sites are not involved in rearrangement, but I will check.
Forum: Illumina/Solexa 11-03-2015, 11:16 AM
Replies: 19
Views: 3,022
Posted By bi_maniac
Thinking about the issue I have remembered that...

Thinking about the issue I have remembered that unability to map against chr14 has meaning because the mutation I am dealing with is a rearrangement (more than 100 pb size). Sorry.
Forum: Illumina/Solexa 11-02-2015, 12:50 PM
Replies: 19
Views: 3,022
Posted By bi_maniac
Execution of BBMap with high_merge case and with...

Execution of BBMap with high_merge case and with chr14.fa as reference (my current computer has only 4GB of memory and was unable to process whole genome).

java...
Forum: Illumina/Solexa 11-02-2015, 11:03 AM
Replies: 19
Views: 3,022
Posted By bi_maniac
OK give me a while, please!

OK give me a while, please!
Forum: Illumina/Solexa 11-02-2015, 10:52 AM
Replies: 19
Views: 3,022
Posted By bi_maniac
Excuse my ignorance. :( Which command you advice...

Excuse my ignorance. :( Which command you advice me to use in order to map to a reference? :confused: I assume there is a possibility to do it with BBMap suite.

In this case I know it is...
Forum: Illumina/Solexa 11-02-2015, 10:45 AM
Replies: 19
Views: 3,022
Posted By bi_maniac
Relevant post from previous thread: " ...

Relevant post from previous thread:

"
Currently I have only been able to perform this task with BBmerge, mergePairs.py and a custom software developed by myself.

I consistently get low...
Forum: Illumina/Solexa 11-02-2015, 10:37 AM
Replies: 19
Views: 3,022
Posted By bi_maniac
YES By the way, it was done with an amplicon...

YES

By the way, it was done with an amplicon library and expected insert size is 300-370
Forum: Illumina/Solexa 11-02-2015, 10:31 AM
Replies: 35
Views: 19,908
Posted By bi_maniac
Hi, helpful people: this conversation continues...

Hi, helpful people: this conversation continues here: http://seqanswers.com/forums/showthread.php?t=63930

Thanks a lot.
Forum: Illumina/Solexa 11-02-2015, 10:25 AM
Replies: 19
Views: 3,022
Posted By bi_maniac
histogram files

histogram files
Forum: Illumina/Solexa 11-02-2015, 10:13 AM
Replies: 19
Views: 3,022
Posted By bi_maniac
Merging paired ends fastq files with BBMerge

This thread comes from http://seqanswers.com/forums/showthread.php?t=6820 but I prefer to start a new one becase there it was a little off topic.

I have two samples, from 2 different patients with...
Forum: Illumina/Solexa 10-30-2015, 10:28 AM
Replies: 35
Views: 19,908
Posted By bi_maniac
Hi Brian, It is amplicon library. Insert...

Hi Brian,

It is amplicon library. Insert range is 300-370. I will send you exec reports soon.
Forum: Illumina/Solexa 10-27-2015, 08:10 PM
Replies: 35
Views: 19,908
Posted By bi_maniac
Dear Brian. I will continue giving you more...

Dear Brian.

I will continue giving you more info as soon as I get it.

Meanwhile let my give you many thanks for your most valuable help. Besides that I want to ask you for a further help:

Do...
Forum: Illumina/Solexa 10-27-2015, 09:46 AM
Replies: 35
Views: 19,908
Posted By bi_maniac
My histogram has 2 peaks in 149-150 and 200 ...

My histogram has 2 peaks in 149-150 and 200

#Mean 166,846
#Median 151
#Mode 200
#STDev 28,597
#PercentOfPairs 16,089
#InsertSize Count
51 1
57 1
Forum: Illumina/Solexa 10-27-2015, 09:23 AM
Replies: 35
Views: 19,908
Posted By bi_maniac
Thanks a lot. You are being very helpful:)

Thanks a lot. You are being very helpful:)
Forum: Illumina/Solexa 10-27-2015, 09:04 AM
Replies: 35
Views: 19,908
Posted By bi_maniac
Thanks. If I understand correctly, given a...

Thanks. If I understand correctly, given a library and a particular gene to be studied, insert size should be known. OK?
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