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Forum: Bioinformatics 06-15-2014, 04:04 PM
Replies: 1
Views: 1,353
Posted By kga1978
..... aaaaand after 3.5h I figured it out - my...

..... aaaaand after 3.5h I figured it out - my good old friend 'read structure'! I forgot to change 101T8B101T to 101T8B8B101T
Forum: Bioinformatics 06-15-2014, 03:25 PM
Replies: 1
Views: 1,353
Posted By kga1978
Question 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: 1,033
Posted By kga1978
Question 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: 1,732
Posted By kga1978
Wow, thanks so much guys - this was incredible...

Wow, thanks so much guys - this was incredible helpful! I got it all covered now :)
Forum: Bioinformatics 11-17-2012, 12:18 PM
Replies: 3
Views: 1,732
Posted By kga1978
Question 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: 11,899
Posted By kga1978
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: 11,899
Posted By kga1978
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: 3,496
Posted By kga1978
Question 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: 7,521
Posted By kga1978
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: 1,219
Posted By kga1978
Question IlluminaBasecallsToSam - specify directory with _barcode.txt files?

Hi All,

I am demultiplexing HiSeq and MiSeq runs using Picard. I have read access to the BaseCalls directory, BUT I can't write to it. Hence when I run 'IlluminaBasecallsToSam' I need to specify...
Forum: 454 Pyrosequencing 05-31-2012, 05:38 AM
Replies: 3
Views: 2,901
Posted By kga1978
The Broad also recently released assembly and...

The Broad also recently released assembly and (common error) cleanup tools for 454 data - I have used them with great success.
...
Forum: Bioinformatics 05-23-2012, 05:14 AM
Replies: 7
Views: 2,730
Posted By kga1978
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: 2,730
Posted By kga1978
Hi GenoMax, I am a little unsure what you...

Hi GenoMax,

I am a little unsure what you mean by that? The files are in standard fasta format.
Forum: Bioinformatics 05-22-2012, 11:58 AM
Replies: 7
Views: 2,730
Posted By kga1978
Ya, I though about that as well, but I have...

Ya, I though about that as well, but I have version 5.2.32 (64bit), so I don't think that is the problem?

K
Forum: Bioinformatics 05-22-2012, 06:13 AM
Replies: 7
Views: 2,730
Posted By kga1978
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: 5,244
Posted By kga1978
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: 5,821
Posted By kga1978
Alright, got it - the first couple of errors were...

Alright, got it - the first couple of errors were indeed caused by the READ_STRUCTURE parameter. Since I used a 151bp PE run the correct format was 151T8B151T. The second problem ('Barcode...
Forum: Bioinformatics 04-25-2012, 06:13 PM
Replies: 4
Views: 5,821
Posted By kga1978
Question 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: 5,266
Posted By kga1978
I use DevonThink pro, which is fantastic but it...

I use DevonThink pro, which is fantastic but it only works for Mac
Forum: Illumina/Solexa 04-12-2012, 04:28 PM
Replies: 1
Views: 8,710
Posted By kga1978
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: 1,790
Posted By kga1978
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: 1,436
Posted By kga1978
I suspected it would be something like this -...

I suspected it would be something like this - crumbs. I'll see if I can get around the problem some other way. Thanks maubp
Forum: Bioinformatics 03-30-2012, 07:17 AM
Replies: 2
Views: 1,436
Posted By kga1978
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: 2,414
Posted By kga1978
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: 2,414
Posted By kga1978
If you can get somebody to help you out with the...

If you can get somebody to help you out with the computer side (which really is necessary for largeish projects), I would suggest trying out the 454 suite developed by the Broad and just released:...
Showing results 1 to 25 of 100

 


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