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Forum: RNA Sequencing 07-11-2017, 10:04 AM
Replies: 4
Views: 3,321
Posted By peromhc
Isn't aggregating the counts from multiple...

Isn't aggregating the counts from multiple transcripts to a single gene kinda the point of tximport? Seems like removing the duplicate gene id's is removing important information.
Forum: Bioinformatics 01-12-2016, 03:49 PM
Replies: 2
Views: 1,526
Posted By peromhc
I had not thought to, but do you think that would...

I had not thought to, but do you think that would be helpful for people?
Forum: Bioinformatics 01-08-2016, 05:08 AM
Replies: 2
Views: 1,526
Posted By peromhc
optimizing transcriptome assembly

Hi All,

I wanted to make sure people have seen the new Oyster River Protocol for transcriptome assembly. In brief, itís an evidence based protocol for optimizing assembly providing...
Forum: RNA Sequencing 08-31-2014, 06:55 PM
Replies: 1
Views: 1,811
Posted By peromhc
The eXpress model explicitly requires multiple...

The eXpress model explicitly requires multiple mappings be included, so you have to use either -a, or something like -k 20. The latter actually, is the preferred method.
Forum: Bioinformatics 08-31-2014, 06:50 PM
Replies: 3
Views: 1,612
Posted By peromhc
I made an amazon machine image for CEGMA - search...

I made an amazon machine image for CEGMA - search CEGMA on AWS and you should find it. It is ami-18935a70. It's preconfigured, just upload your data and run.
Forum: Bioinformatics 08-31-2014, 06:48 PM
Replies: 7
Views: 2,891
Posted By peromhc
I made an amazon machine image for CEGMA - search...

I made an amazon machine image for CEGMA - search CEGMA on AWS and you should find it. It is ami-18935a70. It's preconfigured, just upload your data and run.
Forum: Bioinformatics 07-27-2014, 05:22 PM
Replies: 4
Views: 1,261
Posted By peromhc
For read trimming in RNAseq, please see:...

For read trimming in RNAseq, please see: http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00013/abstract
Forum: RNA Sequencing 07-27-2014, 05:19 PM
Replies: 4
Views: 1,455
Posted By peromhc
Andor, You should consider the quality of...

Andor,

You should consider the quality of your transcriptome assembly as, in my experience, CLC will very often do a poor job of reconstruction. For instance, how many full length transcripts do...
Forum: Literature Watch 03-18-2014, 03:05 AM
Replies: 0
Views: 1,826
Posted By peromhc
On the optimal trimming of high-throughput mRNA sequence data

Here is a new paper that should be of interest to those of us doing de novo transcriptome assembly.

[ABSTRACT]
The widespread and rapid adoption of high-throughput sequencing technologies has...
Forum: Bioinformatics 03-17-2014, 11:24 AM
Replies: 4
Views: 1,334
Posted By peromhc
in bash you can change the location of TMP like...

in bash you can change the location of TMP like this:


export TMPDIR=/path/to/your/tmp


Set TMP before you execute ABySS, and you should be OK to go.
Forum: Bioinformatics 07-30-2013, 12:09 PM
Replies: 4
Views: 1,811
Posted By peromhc
Yes, cat the together! The 2nd should be fine,...

Yes, cat the together! The 2nd should be fine, too BTW, should yield equivalent results.
Forum: Bioinformatics 06-19-2013, 08:51 AM
Replies: 3
Views: 1,019
Posted By peromhc
How did the RNA look at the beginning-- do you...

How did the RNA look at the beginning-- do you have a bioanalyzer trace you could show?

About the assembly, Do you have an idea about the distribution of contig lengths?
Forum: Bioinformatics 06-18-2013, 07:10 PM
Replies: 3
Views: 4,010
Posted By peromhc
see http://samtools.sourceforge.net/mpileup.shtml...

see http://samtools.sourceforge.net/mpileup.shtml


samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
Forum: Bioinformatics 06-18-2013, 07:04 PM
Replies: 3
Views: 1,019
Posted By peromhc
About assembly: Is the assembly from a...

About assembly:

Is the assembly from a single individual of 1 species?
Is there contamination?
How deep is the sequencing?

I assume this is MiSeq sequence data? What is the read quality like?
Forum: Bioinformatics 06-18-2013, 07:00 PM
Replies: 4
Views: 5,299
Posted By peromhc
Also, a BioPython solution. In this case...

Also, a BioPython solution. In this case filtering my length 200nt


#!/usr/bin/python
from Bio import SeqIO
import sys
import os

#usage: python long.seq.py in.fasta out.fasta 200
Forum: Bioinformatics 06-18-2013, 06:48 PM
Replies: 10
Views: 2,324
Posted By peromhc
try filtering out contigs that have a FPKM of...

try filtering out contigs that have a FPKM of less than 1, or .5. This should get rid of a large number of, likely junk, contigs. There are tools in Trinity (RSEM or eXpress) to to this.

Also,...
Forum: Bioinformatics 06-18-2013, 06:45 PM
Replies: 26
Views: 8,377
Posted By peromhc
you don't have jellyfish installed properly. ...

you don't have jellyfish installed properly.

Did you execute the command 'make' inside the Trinity folder that you decompressed after downloading?
Forum: Literature Watch 04-24-2013, 08:34 AM
Replies: 0
Views: 5,277
Posted By peromhc
Improving transcriptome assembly through error correction of high-throughput sequence

Preprint available here: http://arxiv.org/abs/1304.0817
Forum: Bioinformatics 08-04-2012, 10:12 AM
Replies: 4
Views: 4,095
Posted By peromhc
have you installed bowtie?

It seems as if Trinity can't font Bowtie. Do you have it installed and in yout $PATH?

when you type 'which bowtie-build' on the command line, what does it say?

Matt
Forum: Bioinformatics 05-27-2012, 04:26 PM
Replies: 2
Views: 1,262
Posted By peromhc
Have you looked at the ABySS listserve...

Have you looked at the ABySS listserve (https://groups.google.com/forum/?hl=en&fromgroups#!forum/abyss-users). A wealth of info there that you may find useful.
Forum: Bioinformatics 05-21-2012, 06:05 AM
Replies: 2
Views: 2,488
Posted By peromhc
I know that there has been some testing using Ray...

I know that there has been some testing using Ray for metagenome assembly, tho I have never tried it.

Seb567 is the author or Ray, and is active on SeqAnswers-- maybe he will have some insight.
Forum: Sample Prep / Library Generation 05-10-2012, 05:48 AM
Replies: 4
Views: 6,243
Posted By peromhc
If you contact Illumina tech support, they will...

If you contact Illumina tech support, they will send them to you.
Forum: Bioinformatics 05-04-2012, 02:25 PM
Replies: 7
Views: 7,235
Posted By peromhc
yep.. you should check out the git version with...

yep.. you should check out the git version with multithreaded sort -@ flag.. you're doing a lot of sorting!
Forum: Bioinformatics 05-04-2012, 02:19 PM
Replies: 7
Views: 7,235
Posted By peromhc
samtools sort -n sorts by name, not coordinate.....

samtools sort -n sorts by name, not coordinate.. index requires sort by coordinate..
Forum: Bioinformatics 04-09-2012, 03:16 PM
Replies: 9
Views: 5,151
Posted By peromhc
any reason not to update to the latest version of...

any reason not to update to the latest version of samtools.. you're using a pretty old version. That alone may solve your problem

Also, you can use awk/sed/grep to filter results based on...
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