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Forum: Bioinformatics 08-23-2011, 05:51 AM
Replies: 2
Views: 4,932
Posted By James
Predict 5' and 3' UTR's using RNA-seq?

Hi all,

I looked quickly but I couldn't see any threads.

The organism I work on has poorly annotated Untranslated regions (UTRs) There is some EST data I could use, but really I was planning on...
Forum: Sample Prep / Library Generation 06-20-2011, 09:06 AM
Replies: 3
Views: 3,736
Posted By James
2,265.00 makes 48 libraries

2,265.00 makes 48 libraries
Forum: Sample Prep / Library Generation 02-11-2011, 03:52 AM
Replies: 3
Views: 3,736
Posted By James
Making the TruSeq RNA-sample prep kit go further?

Hello all.

We've previously used the mRNA library prep kit, and used 1/4 volumes to make the kit go further and this was fine. What I was wondering was, has anyone done a similar thing with the...
Forum: Bioinformatics 11-16-2010, 12:30 PM
Replies: 7
Views: 3,760
Posted By James
I fixed this problem. It may have been two...

I fixed this problem. It may have been two things:

It may have been calling an older prep_reads I had lurking in my path.

It said I was calling tophat v1.1.0 even though I downloaded v1.1.3. I...
Forum: Bioinformatics 11-15-2010, 05:15 PM
Replies: 8
Views: 5,005
Posted By James
I'm trying to build HTseq (0.4.5p6) from source...

I'm trying to build HTseq (0.4.5p6) from source on mac OSX 10.5.8.

- Using python 2.6.6, GCC 4.01.

when I try to build the package i get this:




python setup.py build
Forum: Bioinformatics 11-15-2010, 09:05 AM
Replies: 7
Views: 3,760
Posted By James
another tophat "could not execute prep_reads" error

Hi,

Im getting this error:


tophat -o RNA-seq-14.11.10/tophat_out_0H -G maygtf.gtf --no-novel-juncs --solexa1.3-quals indexes/_May_2009-masked reads/RNA-seq/R43s_1_sequence_0H.fastq


[Mon...
Forum: Sample Prep / Library Generation 10-25-2010, 01:14 AM
Replies: 6
Views: 4,730
Posted By James
Do you size select??

Hello all,

I am going to be making some paired end libraries very soon.

I have already size selected my DNA prior to going through the library prep protocol, the DNA I have is ~ 50-500bp. So...
Forum: Sample Prep / Library Generation 09-27-2010, 03:15 AM
Replies: 0
Views: 22,055
Posted By James
Multiplexing prep.

Hi,

So we are looking into multiplexing some RNA-seq. Just so I get this right all the samples that you want to multiplex you process each sample separately until after the PCR where you add the...
Forum: Bioinformatics 09-22-2010, 08:37 AM
Replies: 1
Views: 3,325
Posted By James
How to work out coverage?

Hi everyone,

I want to work out what coverage/depth of sequencing we have on our last RNA-seq run. We are working on a small genome, so Ideally we would multiplex to bring the cost down and do...
Forum: Sample Prep / Library Generation 09-16-2010, 10:44 AM
Replies: 4
Views: 2,936
Posted By James
Hi, By PCR enrichment. I mean one of the...

Hi,

By PCR enrichment. I mean one of the last steps in the protocol where you do 10-12 PCR cycles. I just read the protocol in a bit more detail it seems it is actually essential for adding...
Forum: Sample Prep / Library Generation 09-09-2010, 11:49 AM
Replies: 4
Views: 2,936
Posted By James
Paired end Illumina prep problems?

Hi people.

I was wondering if anybody had had any problems with the illumina protocol for making the libraries for paired end sequencing. We previously did some ChIP-seq before (not paired end)...
Forum: Bioinformatics 07-31-2010, 11:48 AM
Replies: 16
Views: 9,490
Posted By James
oh DDB0232428 is chrm1. I'll change that to chrm1...

oh DDB0232428 is chrm1. I'll change that to chrm1 with sed.
Forum: Bioinformatics 07-31-2010, 11:42 AM
Replies: 16
Views: 9,490
Posted By James
Thanks for that. Sorry I am a newbie to this and...

Thanks for that. Sorry I am a newbie to this and perl. How would I go about changing the script to suit my data?

This is my data:



followed by exons after the mRNAs
Forum: Bioinformatics 07-28-2010, 07:04 AM
Replies: 16
Views: 9,490
Posted By James
Hi Brandon, Did you find a simple way to...

Hi Brandon,

Did you find a simple way to convert GFF to GTF. I want to do exactly the same thing, I am also not a programmer.

Thanks, J
Forum: Bioinformatics 07-12-2010, 05:25 AM
Replies: 514
Views: 213,342
Posted By James
Index problem

Hi,

I've been using an index I created for a while now and just realized that the index is only for about half of the fastq file I wanted.

So I carried out bowtie-inspect and I get this:
...
Forum: Bioinformatics 07-05-2010, 08:04 AM
Replies: 7
Views: 4,315
Posted By James
Hi, how did you solve this problem? I get...

Hi, how did you solve this problem?

I get the same error:

tophat -G GFF3/data/gff3/combined.gff --no-novel-juncs indexes/genomic reads/11.3.10/R43s_4_sequence.fastq

[Sun Jul 4 16:24:40 2010]...
Forum: Bioinformatics 07-04-2010, 10:38 AM
Replies: 5
Views: 2,760
Posted By James
Hi, I downloaded the GFF from the database...

Hi,

I downloaded the GFF from the database for my organism

http://dictybase.org/Downloads/

take a look at the formatting?

Cheers, J
Forum: Bioinformatics 07-04-2010, 09:14 AM
Replies: 5
Views: 2,760
Posted By James
Tophat/Cufflinks using own GFF3 file problems

Hi people.

I'm having a couple of problems with aligning using my own junctions in a GFF3 file. I'm just starting out with this just so I can make this simple and just look at changes in gene...
Forum: Bioinformatics 05-17-2010, 02:37 AM
Replies: 13
Views: 5,468
Posted By James
I have tried to Install this on Mac however I...

I have tried to Install this on Mac however I seem unable to. I have moved all the bowtie files and installed Python. I get stuck on this bit:

./configure --prefix=/path/to/install/directory/

I...
Forum: Bioinformatics 05-06-2010, 01:22 PM
Replies: 7
Views: 5,751
Posted By James
Thanks guys RPKM/FPKM is where I'm stumbling...

Thanks guys RPKM/FPKM is where I'm stumbling currently. Will try some of those out.

Thanks, J
Forum: Bioinformatics 05-05-2010, 10:51 AM
Replies: 7
Views: 5,751
Posted By James
Starting out with mRNA-seq analysis

So I'm a newbie to this so have a few questions on what programs to use (just to get me started) that are good for the beginner, I've had a good look through the list of programs but I'd like some...
Forum: Bioinformatics 04-13-2010, 02:12 AM
Replies: 36
Views: 23,914
Posted By James
I'm having a similar problem to Ben, I have...

I'm having a similar problem to Ben, I have illumina fastq files that are gzipped. I can upload them in a few minutes but then when I try to do the groomer i get this error:

An error occurred...
Forum: Bioinformatics 03-30-2010, 12:38 AM
Replies: 514
Views: 213,342
Posted By James
Tutorial - Build a new index

Hi guys,

I'm new to seqanswers and to alignment. So I started using bowtie as it seems to have a good reputation manual and tutorial.

I am working through the tutorial, I have got to the point...
Showing results 1 to 23 of 23

 


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