Forum: Bioinformatics
06-15-2014, 04:04 PM
|
|
Replies: 1
Views: 1,385
|
|
Forum: Bioinformatics
06-15-2014, 03:25 PM
|
|
Replies: 1
Views: 1,385
Demultiplexing problem
Hi All,
I have been trying to demultiplex some Illumina (101bp PE, dual barcoded) libraries using Picard - e.g.:
java -Xmx2g -jar /seq/software/picard/1.626/bin/ExtractIlluminaBarcodes.jar...
|
|
Forum: Bioinformatics
01-30-2013, 01:21 PM
|
|
Replies: 0
Views: 1,075
Error in IlluminaBasecallsToSam.jar
Hi All,
I run the following command
java -Xmx2g -Dsnappy.disable=true -jar /idi/sabeti-scratch/kandersen/bin/picard/IlluminaBasecallsToSam.jar...
|
|
Forum: Bioinformatics
11-17-2012, 03:32 PM
|
|
Replies: 3
Views: 1,778
|
|
Forum: Bioinformatics
11-17-2012, 12:18 PM
|
|
Replies: 3
Views: 1,778
Extracting all microbial sequences from NT
Hi all,
I have been trying to find a way to extract all microbial (and eukaryotic) sequences in the NT database but I am running into a bunch of problems.
I have tried to download the GI lists...
|
|
Forum: Bioinformatics
08-12-2012, 06:07 AM
|
|
Replies: 29
Views: 12,199
That would probably have done the job, but...
That would probably have done the job, but unfortunately we don't have Biopython installed on our cluster so I can't run it (same with Bioperl).
What I am looking for is basically a standalone...
|
|
Forum: Bioinformatics
08-11-2012, 12:59 PM
|
|
Replies: 29
Views: 12,199
Hi All,
I have exactly this problem as well,...
Hi All,
I have exactly this problem as well, but with fasta files. Anybody know of a program that will work with Fasta or could modify 'mergeShuffledFastqSeqs.pl' so it would work on that format...
|
|
Forum: Bioinformatics
07-27-2012, 02:26 PM
|
|
Replies: 2
Views: 3,570
MEGAN command line without X11?
Hi all,
I just install Mac OS 10.8 and it turns out that X11 is no longer part of the install. I have been running MEGAN via X11 in the past (command line), but I'm wondering if there is a way to...
|
|
Forum: Bioinformatics
06-13-2012, 05:20 AM
|
|
Replies: 16
Views: 7,682
Hi Andreas,
Do I understand the following...
Hi Andreas,
Do I understand the following correctly. If I have a reference fasta with two segments (from a virus), do I need to split those two segments into separate fasta files and run them each...
|
|
Forum: Bioinformatics
06-11-2012, 02:58 PM
|
|
Replies: 0
Views: 1,247
|
|
Forum: 454 Pyrosequencing
05-31-2012, 05:38 AM
|
|
Replies: 3
Views: 2,961
|
|
Forum: Bioinformatics
05-23-2012, 05:14 AM
|
|
Replies: 7
Views: 2,780
Hi maubp,
I'll try out your suggestions -...
Hi maubp,
I'll try out your suggestions - this happened to me using several different fasta files though, so I'm wondering whether something else is going on. Thanks for the suggestions - much...
|
|
Forum: Bioinformatics
05-22-2012, 01:20 PM
|
|
Replies: 7
Views: 2,780
|
|
Forum: Bioinformatics
05-22-2012, 11:58 AM
|
|
Replies: 7
Views: 2,780
|
|
Forum: Bioinformatics
05-22-2012, 06:13 AM
|
|
Replies: 7
Views: 2,780
Usearch error - "Sequence too long"
Hi All,
I am trying to create a usearch udb database of hg19 using the following:
usearch -makeudb hg19.fasta --output hg19.udb -slots 400000009 -w 16 -id 0.90
However, I keep getting this...
|
|
Forum: Bioinformatics
05-03-2012, 11:38 AM
|
|
Replies: 2
Views: 5,306
Have a look at this
...
Have a look at this
http://seqanswers.com/forums/showthread.php?t=17974
I have been using this:
http://seqanswers.com/forums/attachment.php?attachmentid=1238&d=1330350938
|
|
Forum: Bioinformatics
04-25-2012, 08:18 PM
|
|
Replies: 4
Views: 5,934
|
|
Forum: Bioinformatics
04-25-2012, 06:13 PM
|
|
Replies: 4
Views: 5,934
Demultiplexing MiSeq run - problems
Hi All,
I just got a MiSeq run back from our core and I am trying to demultiplex everything. However, I have received no instructions as to how I do this, so I am a bit in the dark. The run was...
|
|
Forum: General
04-19-2012, 08:49 AM
|
|
Replies: 11
Views: 5,404
|
|
Forum: Illumina/Solexa
04-12-2012, 04:28 PM
|
|
Replies: 1
Views: 8,825
Carrier RNA and Illumina sequencing
Hi All,
We have recently experienced a lot of problems with our RNA library preps when using samples containing a large amount of Qiagen carrier RNA (poly-A, 100bp-10kb in length). Specifically,...
|
|
Forum: Bioinformatics
03-30-2012, 03:43 PM
|
|
Replies: 2
Views: 1,831
PairedreadFinder or similar?
Hi,
I have two fastq files that originated from a matched paired-end library (mate-pair1.fastq and mate-pair2.fastq), but I have now trimmed them and they contain different numbers of reads and...
|
|
Forum: Bioinformatics
03-30-2012, 01:30 PM
|
|
Replies: 2
Views: 1,477
|
|
Forum: Bioinformatics
03-30-2012, 07:17 AM
|
|
Replies: 2
Views: 1,477
Getting reads from lastal results?
Hi All,
I have a bunch of paired-end reads and I aligned them against a custom database (viruses) using LASTAL:
lastal -Q1 /idi/sabetilab/kandersen/references/blast/arena...
|
|
Forum: Bioinformatics
03-06-2012, 04:07 PM
|
|
Replies: 5
Views: 2,460
Install the trial versions of CLC Genome...
Install the trial versions of CLC Genome Workbench and Geneious. They both align 454 data quite well and you can make up your mind of which one you like the most.
Both programs are also user...
|
|
Forum: Bioinformatics
03-05-2012, 05:06 PM
|
|
Replies: 5
Views: 2,460
|
