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Search: Posts Made By: flyingoyster
Forum: Bioinformatics 12-16-2013, 04:58 PM
Replies: 1
Views: 1,324
Posted By flyingoyster
how to get ungapped alignment from BWA?

I am dealing with some RNA-seq data. First, I assemblied the short reads to contigs using Trinity, and then map the short reads to the contigs using BWA. I would like to get ungapped alignment from...
Forum: RNA Sequencing 11-19-2013, 05:12 PM
Replies: 6
Views: 2,601
Posted By flyingoyster
I used the other denovo assembly for our species...

I used the other denovo assembly for our species and got the similar mapping results using paired-end. That's really frustrating.
The commands I used for Trinity and Bowtie are:
Trinity assembly:...
Forum: RNA Sequencing 11-18-2013, 06:17 AM
Replies: 3
Views: 1,965
Posted By flyingoyster
I had similar problem, but even lower mapping...

I had similar problem, but even lower mapping rate (about 2%). What could be the problem? If you figure it out, please let know. Thanks!
Forum: RNA Sequencing 11-14-2013, 05:11 PM
Replies: 6
Views: 2,601
Posted By flyingoyster
Hi Wallysb01, I checked the quality of reads...

Hi Wallysb01,
I checked the quality of reads got from Illumina. They are good. I didn't trim the reads, so all 100bp paired-end reads are used for building assembly and mapping step. I had strand...
Forum: RNA Sequencing 11-13-2013, 08:02 PM
Replies: 6
Views: 2,601
Posted By flyingoyster
Very low map rate while mapping to denovo assebly

Hi everyone,

I am working on a species with little genome information available. I had 4 samples of RNA-seq. I would like to know how many genes were differentially expressed among these 4...
Forum: Bioinformatics 09-03-2013, 12:21 AM
Replies: 5
Views: 3,052
Posted By flyingoyster
@Simon Anders, Yes, My data is paired-end. If...

@Simon Anders, Yes, My data is paired-end. If HTseq-count counts read pairs, not reads, that makes sense. Thanks a lot!
@dpryan, I used Galaxy server, so not be able to choose options.

If I...
Forum: Bioinformatics 09-02-2013, 05:13 PM
Replies: 5
Views: 3,052
Posted By flyingoyster
Assuming that the file I used for input of...

Assuming that the file I used for input of HTseq-count includes the unaligned reads in the output BAM file, But the number of "no_alignment" reads doesn't match the number of reads not mapped to the...
Forum: Bioinformatics 09-01-2013, 10:17 PM
Replies: 5
Views: 3,052
Posted By flyingoyster
"not_aligment" from the output of HTseq-count

What's the meaning of "not_alignment" from the output of HTseq-count? The manual says it is the "reads in the Sam/Bam file without alignment". Does this mean the reads that are not mapped to the...
Forum: Illumina/Solexa 08-12-2011, 11:54 AM
Replies: 28
Views: 15,066
Posted By flyingoyster
Smile RADseq

Anyone knows well about Restriction-Associated-DNA sequencing? I read a lot of papers about this. It seems that this will produce thousands of markers in very short time. I wonder someone here is...
Forum: Introductions 08-05-2011, 01:26 PM
Replies: 0
Views: 698
Posted By flyingoyster
Hello everyone

Hi everyone, I am a graduate student, studying marine biology. I am working on NGS, and some headache comes with the excitement. I would love to discuss with you. :)
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