SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 9 of 9
Search took 0.00 seconds.
Search: Posts Made By: selen
Forum: Bioinformatics 10-17-2013, 11:27 AM
Replies: 4
Views: 2,347
Posted By selen
Anybody tried to use different length reads for...

Anybody tried to use different length reads for R1 and R2 for aligning their PE data? Any concerns tophat may not be able to handle?

Due to quality issues I had to trim the last 50bp of a R2 of a...
Forum: Bioinformatics 03-13-2013, 09:19 AM
Replies: 4
Views: 2,373
Posted By selen
Any luck in getting CASAVA variants into VCF...

Any luck in getting CASAVA variants into VCF format????
Forum: SOLiD 12-13-2012, 10:57 AM
Replies: 1
Views: 1,337
Posted By selen
Lifescope smallRNA module with mouse genome

Has anybody had any luck in running in smallRNA module for Lifescope for mouse genome. ?

I've been using the input files I downloaded from mirbase (miRNA.txt for mature, mmu.gff2/mmu.gff3 for...
Forum: Bioinformatics 12-02-2011, 09:10 AM
Replies: 12
Views: 5,930
Posted By selen
Thumbs up I'm glad you all figured it out. I had the same...

I'm glad you all figured it out. I had the same problem and now it works with "-o ./" setting..Thanks!!!!
Forum: Bioinformatics 11-14-2011, 08:44 AM
Replies: 20
Views: 8,915
Posted By selen
A single bam file as alignment output

Dear Semyon,

Is there a way to get alignments in a single file per sample in bam format as alignment output?

As far as I know we need an additional "configurebuild --targets sort bam " step to...
Forum: Bioinformatics 01-20-2011, 11:51 AM
Replies: 89
Views: 55,127
Posted By selen
Semyon, Within the sample folder, the name...

Semyon,

Within the sample folder, the name of each fastq file provides the sample, index, lane and read information. What about the last three digit (001, 002..)? Do they represent the repeated...
Forum: Bioinformatics 01-20-2011, 06:58 AM
Replies: 89
Views: 55,127
Posted By selen
Thanks Semyon, sample sheet is the key to my...

Thanks Semyon, sample sheet is the key to my question. I assume you give this file as an input along with the config.txt while running bclconverter with the alignment option. Or is it something else?...
Forum: Bioinformatics 01-19-2011, 01:18 PM
Replies: 89
Views: 55,127
Posted By selen
Semyon, Can you please post more information...

Semyon,

Can you please post more information about the directory structure and how you set it up by project/sample names?

Thanks
Selen
Forum: Bioinformatics 01-19-2011, 11:43 AM
Replies: 1
Views: 2,876
Posted By selen
The following awk script converts sorted file to...

The following awk script converts sorted file to BED format that has 4 fields. You can update the script as you need...

# sortedToBed.awk
# Input : SORTED FILE
# Output : <Chromosome> <start...
Showing results 1 to 9 of 9

 


All times are GMT -8. The time now is 06:45 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO