SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 15 of 15
Search took 0.00 seconds.
Search: Posts Made By: Ash
Forum: Bioinformatics 09-18-2012, 07:14 AM
Replies: 1
Views: 3,109
Posted By Ash
Adventures with installing blat on Mac OS X

Hi all,

I have a number of reads (10000) that I need to blat against the human genome. So I decided installing standalone blat on my Mac Pro 4,1 would be the way forward. I first downloaded the...
Forum: Bioinformatics 10-12-2011, 02:21 AM
Replies: 2
Views: 1,447
Posted By Ash
Many thanks for your prompt response, swbarnes2....

Many thanks for your prompt response, swbarnes2. I'd gotten as far as having to do 2 searches using :

samtools view -f 3 -F 1564 my.bam chr:500-1000 > forward.sam
samtools view -f 19 -F 1548...
Forum: Bioinformatics 10-11-2011, 10:49 AM
Replies: 2
Views: 1,447
Posted By Ash
Searching for paired reads around a location

Hi folks,

I'm looking at the 1000 genomes data using samtools. So far the flag filter has been great in helping me locate regions of interest, but for what I want to do next, I'm not sure this is...
Forum: Bioinformatics 09-15-2011, 06:03 AM
Replies: 6
Views: 5,411
Posted By Ash
Thanks swbarnes2. I was hoping there was a way of...

Thanks swbarnes2. I was hoping there was a way of specifying more than one position at a time, but I guess I can get round that with a perl script.

All the best,

A
Forum: Bioinformatics 09-14-2011, 05:31 AM
Replies: 6
Views: 5,411
Posted By Ash
Aaaah... now I see! So everything has to be...

Aaaah... now I see! So everything has to be searched from the flag field, and using -f and -F should give you every possible combination you need (with there being some redundancy in the system).
...
Forum: Bioinformatics 09-12-2011, 05:53 AM
Replies: 6
Views: 5,411
Posted By Ash
Many thanks for your response swbarnes2. I should...

Many thanks for your response swbarnes2. I should have picked up on -F being the opposite of -f! I've been playing around with what you suggested and a few more questions if I may:

1) Using your...
Forum: Bioinformatics 09-09-2011, 08:13 AM
Replies: 6
Views: 5,411
Posted By Ash
Finding reads where the mate is unmapped

Hi folks,

Apologies in advance for the rambling post!

Out of the paired end reads in the 1000 genomes data, I am trying to locate those reads where one end of the pair is unmapped. I understand...
Forum: Bioinformatics 10-28-2010, 07:20 AM
Replies: 2
Views: 3,580
Posted By Ash
Many thanks for your response drio. I think it...

Many thanks for your response drio. I think it may take me some time deciphering the intricacies of the flag field (a good few posts to read on this site!), so I'll be back with more dumb questions...
Forum: Bioinformatics 10-28-2010, 03:59 AM
Replies: 2
Views: 3,580
Posted By Ash
Finding unmapped reads using samtools

Hi guys,

Samtools is truly amazing! However, there's a couple of things I was wondering about...

Is there any way of pulling out those reads in a bam file, using samtools, where one pair of the...
Forum: Bioinformatics 10-01-2010, 05:29 AM
Replies: 1
Views: 2,400
Posted By Ash
Problem solved! It wasn't liking the "chr5" bit -...

Problem solved! It wasn't liking the "chr5" bit - this is 1000 genomes data and they just use 5 instead of chr5.
Forum: Bioinformatics 10-01-2010, 03:28 AM
Replies: 1
Views: 2,400
Posted By Ash
Help with Samtools "view"

Hi guys,

Apologies up front if this is a stupid question... I've been using the following to view areas of bam alignments, which is really convenient as it allows me to check that my region of...
Forum: Bioinformatics 08-23-2010, 05:14 AM
Replies: 2
Views: 2,893
Posted By Ash
Many thanks for your response. The...

Many thanks for your response.

The parameters are identical in the 2 searches (online and standalone) - I think perhaps the difference is that I'm using legacy blast and not the BLAST+ that the...
Forum: Bioinformatics 08-19-2010, 07:42 AM
Replies: 2
Views: 2,893
Posted By Ash
Help with Standalone Blast

Hi all,

I have managed to install standalone blast on my computer and it appears to be working correctly. The output file I get (and I have tried a number of different options) never tells me the...
Forum: Bioinformatics 06-29-2010, 01:56 AM
Replies: 7
Views: 5,513
Posted By Ash
Success! Thanks for the tip folks. A

Success! Thanks for the tip folks.

A
Forum: Bioinformatics 06-28-2010, 08:06 AM
Replies: 7
Views: 5,513
Posted By Ash
Help with installing samtools on a Mac

Hi,

I'm fairly new to Unix (and bioinformatics generally!). I'm trying to open .bam files, and thought samtools might be the way forward. However, I'm struggling to get it working.

I downloaded...
Showing results 1 to 15 of 15

 


All times are GMT -8. The time now is 03:06 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO