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Forum: Bioinformatics 10-30-2015, 02:44 PM
Replies: 651
Views: 134,357
Posted By rocksd
Thanks Brian! What if I use BBSplit? How...

Thanks Brian!

What if I use BBSplit? How many genomes can BBsplit handle? What I ultimately want to do is to figure out how many reads mapped to each genome and separate those reads by genome...
Forum: Bioinformatics 10-30-2015, 11:10 AM
Replies: 651
Views: 134,357
Posted By rocksd
Hi Brian, Thanks a lot for your quick...

Hi Brian,

Thanks a lot for your quick response!

Perhaps you can give me some advice: I have a metagenomic sequencing fast file. I want to know how many reads are mapped to each of the viral...
Forum: Bioinformatics 10-30-2015, 07:10 AM
Replies: 651
Views: 134,357
Posted By rocksd
Hi Brian, I am using bbmap.sh to evaluate...

Hi Brian,

I am using bbmap.sh to evaluate coverage on a collection of viral genomes (viral all.fna downloaded from NCBI). The command I am using is as follow:

bbmap.sh in=XXX.fastq...
Forum: Illumina/Solexa 07-22-2015, 01:45 PM
Replies: 7
Views: 6,390
Posted By rocksd
Brian, Thanks for your reply. Are those...

Brian,

Thanks for your reply. Are those bar-codes (that were misread) from Illumina or are they custom ones that prepared by you or your end-user?

Thanks

James
Forum: Illumina/Solexa 07-22-2015, 01:29 PM
Replies: 6
Views: 1,824
Posted By rocksd
Hi Hilary, Thank you very much for the quick...

Hi Hilary,

Thank you very much for the quick reply and the quality information! It is very helpful.

James
Forum: Illumina/Solexa 07-22-2015, 08:39 AM
Replies: 7
Views: 6,390
Posted By rocksd
Hi Brian, We are looking to purchasing a...

Hi Brian,

We are looking to purchasing a NextSeq. But we do have a concern regarding the quality of the reads generated on NextSeq. Do you have a better experience now with the NextSeq?

Your...
Forum: Illumina/Solexa 07-22-2015, 08:34 AM
Replies: 6
Views: 1,824
Posted By rocksd
Hi HMorrison, Are you satisfied with the...

Hi HMorrison,

Are you satisfied with the quality of the NextSeq run? How does it compared to your HiSeq runs?

Kindly share your experience with us and thanks!

James
Forum: General 09-02-2011, 05:32 AM
Replies: 3
Views: 1,903
Posted By rocksd
How long (bp) are those loci? If it is short...

How long (bp) are those loci? If it is short enough, I'd say perform multiplex PCR using primers embedded with nextgen adaptors. In this case, sample prep cost may be significantly lower. You can...
Forum: General 09-02-2011, 05:18 AM
Replies: 6
Views: 2,370
Posted By rocksd
I just sent a personal email to you so if you...

I just sent a personal email to you so if you wish you can contact me as I am dealing with a similar request.

Rocksd
Forum: Sample Prep / Library Generation 05-07-2011, 07:05 PM
Replies: 11
Views: 5,221
Posted By rocksd
One possibility is the design of your index...

One possibility is the design of your index sequences. How long are your index sequences and how different they are? How many samples did you pool into one lane? What version of Illumina SCS...
Forum: Literature Watch 10-15-2010, 01:31 PM
Replies: 11
Views: 4,291
Posted By rocksd
Hi greenshell, I am about to use MapSplice...

Hi greenshell,

I am about to use MapSplice as I want to look at non-canonical splice sites. But I have a few questions:

1. Do I have to build Bowtie index for every chr individually? I guess...
Forum: Bioinformatics 10-15-2010, 09:43 AM
Replies: 6
Views: 4,394
Posted By rocksd
I believe you need to remove the "," between the...

I believe you need to remove the "," between the two sequencing file if they are from two different samples.
Forum: Illumina/Solexa 10-06-2010, 11:28 AM
Replies: 3
Views: 1,844
Posted By rocksd
Unhappy RTA hangs in the middle of GAIIX run

We started a PE run but to my dismay RTA stopped in the middle of the run. After the first read, we stop the run and restarted RTA but it did not help. We reinstalled RTA and start RTA again but it...
Forum: Bioinformatics 07-22-2010, 01:32 PM
Replies: 4
Views: 3,112
Posted By rocksd
Cole, Did you fix this bug? I am running...

Cole,

Did you fix this bug?
I am running a Cuffdiff on two pig samples and ended up with Segment error. I then checked the combined_transcript.gtf file generated in Cuffcompare but did not...
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