SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 62
Search took 0.02 seconds.
Search: Posts Made By: Apexy
Forum: Bioinformatics 11-12-2015, 04:43 AM
Replies: 4
Views: 709
Posted By Apexy
I agree with @GenoMax Trimming can be...

I agree with @GenoMax
Trimming can be potentially detrimental http://goo.gl/CG6eTl
Forum: Bioinformatics 06-03-2014, 03:29 AM
Replies: 3
Views: 2,785
Posted By Apexy
Hi eagb, Is this exercise an attempt to...

Hi eagb,

Is this exercise an attempt to reduce redundancy or complexity of the transcriptome assembly? Out of curiosity, what are the odds that the largest sequence per 'gene' is a chimera or ...
Forum: Bioinformatics 03-26-2014, 10:04 PM
Replies: 15
Views: 4,012
Posted By Apexy
Hi, I remember you can compile velveth with...

Hi,

I remember you can compile velveth with "OPENMP=1" to make use of multithreading. Kindly go through the velvet mailing list for a more technical details.

HTH
Forum: RNA Sequencing 03-16-2014, 11:06 PM
Replies: 3
Views: 1,575
Posted By Apexy
Hi, To add to what dongilbert suggested, I...

Hi,
To add to what dongilbert suggested, I would say that care has to be taken when performing post-assembly clustering or re-assembly (across multiple kmers or assemblies from different...
Forum: Bioinformatics 03-06-2014, 09:10 PM
Replies: 22
Views: 2,752
Posted By Apexy
Hi, Just another line of thought for trimming...

Hi,
Just another line of thought for trimming or not http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00017/full
Forum: RNA Sequencing 03-06-2014, 09:06 PM
Replies: 15
Views: 3,984
Posted By Apexy
Hi Zapages and other, If you plan on...

Hi Zapages and other,
If you plan on performining a de novo assembly of the trimmed reads, it may be good for you to have a look at this paper....
Forum: Bioinformatics 03-01-2014, 01:24 AM
Replies: 2
Views: 1,001
Posted By Apexy
This is quite an old thread but you may consider...

This is quite an old thread but you may consider novel perpectives when you engage with future datasets. If it is RNA-Seq you are dealing with, take a look at this paper...
Forum: Bioinformatics 01-17-2014, 03:07 AM
Replies: 15
Views: 4,012
Posted By Apexy
Probably dependent on the size of the target...

Probably dependent on the size of the target genome, the assembly algorithm; size, type and quality of input data. The following places might be of help...
Forum: Bioinformatics 10-28-2013, 07:38 AM
Replies: 1
Views: 1,151
Posted By Apexy
Hi, Kindly upload a sample of both files...

Hi,
Kindly upload a sample of both files (scafSeq.FG.fill and genome-assoc-chromosomes.txt). Without the fasta file, I am wondering how the following:
while (<FASTA>){
my $line = $_;
chomp...
Forum: Bioinformatics 10-25-2013, 12:48 AM
Replies: 2
Views: 982
Posted By Apexy
Hi, I have never stored short read alingments...

Hi,
I have never stored short read alingments in a bed file. I have used the SAM format to store my reads, then use a bed file which have coordinates of those regions I want to extract reads from....
Forum: Bioinformatics 09-24-2013, 01:29 PM
Replies: 4
Views: 1,892
Posted By Apexy
Hi Mutagenic, I am aware that in bowtie, there...

Hi Mutagenic,
I am aware that in bowtie, there is an option (--nofw/--norc) which can allows you do this type of thing but I have not used it. It is possible that other alignment tools might have a...
Forum: Bioinformatics 09-23-2013, 10:48 PM
Replies: 4
Views: 1,892
Posted By Apexy
Hi, What are you referring to by strand...

Hi,

What are you referring to by strand bias? Is this same as the mapping orientation? Do you wish to constrain reads so that they map to one strand and not the other?
Forum: Bioinformatics 09-20-2013, 12:18 AM
Replies: 6
Views: 1,795
Posted By Apexy
Hi ej_duncan, The best would be for you to ask...

Hi ej_duncan,
The best would be for you to ask your collaborator. On second thought, this contains components of a FASTQ file that has been transform to some kind of tab format.

HTH
Forum: Bioinformatics 09-20-2013, 12:09 AM
Replies: 6
Views: 2,146
Posted By Apexy
Hi capricy, I was requesting for the name of...

Hi capricy,
I was requesting for the name of the database. Can you also provide the URL to the data-sets which you've downloaded? I should take a look at it. Like I mention earlier, in the absence...
Forum: Bioinformatics 09-20-2013, 12:07 AM
Replies: 6
Views: 2,146
Posted By Apexy
Hi capricy, I was requesting for the name of...

Hi capricy,
I was requesting for the name of the database. Can you also provide the URL to the data-sets which you've downloaded? I should take a look at it. Like I mention earlier, in the absence...
Forum: Bioinformatics 09-19-2013, 09:50 AM
Replies: 6
Views: 2,146
Posted By Apexy
Hi, Which database are you refering to? You...

Hi,
Which database are you refering to? You make have to look carefully as some databases provide annotation files which would have information about location of the CDS on the genome. It may be of...
Forum: Bioinformatics 08-29-2013, 05:44 AM
Replies: 4
Views: 1,465
Posted By Apexy
@ bishwo, You are correct. Without diverting...

@ bishwo,
You are correct. Without diverting @arkilis, it is also possible to know the similarity between one or many sequences without explicitly aligning them as it is the case with tools that...
Forum: Bioinformatics 08-28-2013, 10:52 PM
Replies: 4
Views: 1,465
Posted By Apexy
They are different. However, it has become very...

They are different. However, it has become very difficult to dissociate them because when attempting to achieve something involving one of them, it is unlikely to avoid the other. To me, this...
Forum: Bioinformatics 08-27-2013, 08:39 AM
Replies: 3
Views: 879
Posted By Apexy
Try: grep -wiv -f list.txt uniprot.fasta >...

Try:
grep -wiv -f list.txt uniprot.fasta > out
Forum: Bioinformatics 06-11-2013, 02:58 AM
Replies: 2
Views: 1,497
Posted By Apexy
Hi, I noticed your query has note attended to....

Hi,
I noticed your query has note attended to. Let me attempt a learners non-specialist answer. if I remember well, there are a number of executables in the hmmer package to achieve different...
Forum: Bioinformatics 05-20-2013, 01:35 AM
Replies: 4
Views: 4,910
Posted By Apexy
Hi Dsher, I don't have a direct answer for...

Hi Dsher,

I don't have a direct answer for this as I have not used blastdbcmd lately. Could the problem be related to this? Let me know if this helps while waiting from someone who is familiar...
Forum: Bioinformatics 05-20-2013, 12:24 AM
Replies: 4
Views: 4,910
Posted By Apexy
Its likely that this issue has already been...

Its likely that this issue has already been address here: http://seqanswers.com/forums/showthread.php?t=22415

HTH
Forum: Bioinformatics 04-29-2013, 02:58 AM
Replies: 7
Views: 1,683
Posted By Apexy
This would have been an appealing solution if...

This would have been an appealing solution if each sequence had only one GO term.
Forum: Bioinformatics 04-29-2013, 02:49 AM
Replies: 7
Views: 1,683
Posted By Apexy
Hi, Its better as you have not done any...

Hi,
Its better as you have not done any clustering on them before annotation since de novo clustering sometimes assigns different transcripts from paralogous gene into the same clusters and for...
Forum: Bioinformatics 04-29-2013, 01:49 AM
Replies: 7
Views: 1,683
Posted By Apexy
Thumbs up Hi, Out of curiosity, are these (10000)...

Hi,
Out of curiosity, are these (10000) sequences already clusetered (de novo clustering) or do they represent only sequences with GO from your assembly?

I had writen something down exactly as...
Showing results 1 to 25 of 62

 


All times are GMT -8. The time now is 07:42 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO