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Forum: Sample Prep / Library Generation 05-09-2016, 08:28 AM
Replies: 15
Views: 20,324
Posted By rcook34
Hey all, Sorry to reopen this older thread,...

Hey all,

Sorry to reopen this older thread, but I was curious if anyone had anything else to add? I am very interested in this area, since my experiments using both NEB's and an in-house Klenow...
Forum: Bioinformatics 01-27-2016, 03:27 PM
Replies: 5
Views: 1,648
Posted By rcook34
Command looks good to me... Can you share...

Command looks good to me...

Can you share some detail about your workflow? ie not sure how you're going from a sorted bam file to fastq then trimming then (re)alignment... Is this data you found...
Forum: Bioinformatics 01-27-2016, 12:43 PM
Replies: 5
Views: 1,648
Posted By rcook34
Can you show us your full bowtie2 command? For...

Can you show us your full bowtie2 command? For exome-seq data to hg19 I always tend to get mapping rates > 95%, so I would think there is clearly a problem here. At first glance it looks like the...
Forum: Bioinformatics 12-11-2015, 10:55 AM
Replies: 6
Views: 5,403
Posted By rcook34
Thanks for the help! I was successful with...

Thanks for the help! I was successful with blancha's command, I do also want to try rwan's command as well when I get some time to look at this more next week.

blancha: I do have a follow up if...
Forum: Bioinformatics 12-09-2015, 03:51 PM
Replies: 6
Views: 5,403
Posted By rcook34
For loop in bash terminal to concatenate fastq files

Hi all,

I am trying to create a bash command to use a for loop to concatenate fastq files split by lanes after demultiplexing. For example, after demultiplexing, my non-concatenated fastq files...
Forum: Bioinformatics 11-29-2012, 12:30 PM
Replies: 1
Views: 1,325
Posted By rcook34
Solution

I found out it was a bad set of data. Used bowtie2 to map a completely different set of mate pair data and it worked as it should. Seriously though, a few weeks and 132 views and no one responds?...
Forum: Bioinformatics 11-06-2012, 07:53 AM
Replies: 1
Views: 1,325
Posted By rcook34
Smile Bowtie giving opposite results

Hi all,

I am using the bowtie program to run alignments on a set of mate pair data (2 fastq files) and have run into a problem. What I have found is that if I run bowtie with the regular fastq...
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