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Search: Posts Made By: jimmybee
Forum: Bioinformatics 06-06-2014, 02:00 AM
Replies: 118
Views: 42,611
Posted By jimmybee
Ive been using it over the last couple of weeks...

Ive been using it over the last couple of weeks and it has been really quick. Im actually using it to run adapter trimming (with small inserts, all of your reads should overlap), so adding in some...
Forum: Bioinformatics 02-14-2014, 07:01 PM
Replies: 1
Views: 712
Posted By jimmybee
What error message?

What error message?
Forum: Bioinformatics 02-09-2014, 02:50 PM
Replies: 2
Views: 960
Posted By jimmybee
Generally its 25bp. A 20mer will map to a variety...

Generally its 25bp. A 20mer will map to a variety of different genomes, if given the chance, whereas 25mers are more stringent are more likely to be "real" when mapped to your closest reference.
Forum: Bioinformatics 12-04-2013, 01:15 PM
Replies: 3
Views: 1,565
Posted By jimmybee
This isn't an error, its a limitation. A lot of...

This isn't an error, its a limitation. A lot of applications of genome sequencing calls for sequencing a fragment shorter than the read-length (e.g. aDNA, small-RNAs). Adapter trimming corrects for...
Forum: Bioinformatics 11-26-2013, 01:55 PM
Replies: 6
Views: 1,992
Posted By jimmybee
Have a look at any paper that constructs whole...

Have a look at any paper that constructs whole chloroplasts and there should be methods to make them. From memory, I think this paper uses a particular assembly strategy to make whole chloroplasts in...
Forum: Bioinformatics 11-26-2013, 01:44 PM
Replies: 3
Views: 1,094
Posted By jimmybee
Completely depends on the size of your datasets. ...

Completely depends on the size of your datasets.

In my opinion, if you have a sizeable cluster to connect to, a desktop is going to be a complete waste of money. I haven't used a desktop computer...
Forum: Bioinformatics 11-22-2013, 08:23 PM
Replies: 9
Views: 5,934
Posted By jimmybee
For BLASTX use pauda ...

For BLASTX use pauda

http://ab.inf.uni-tuebingen.de/software/pauda/
Forum: Bioinformatics 11-22-2013, 08:01 PM
Replies: 2
Views: 1,144
Posted By jimmybee
NCBI SRA database

NCBI SRA database
Forum: Bioinformatics 11-06-2013, 01:32 PM
Replies: 4
Views: 2,749
Posted By jimmybee
Are there dependencies for ReadsToTranscripts,...

Are there dependencies for ReadsToTranscripts, GraphFromFasta, QuantifyGraph and Chrysalis Installation? That would suggest why some installed and those failed....
Forum: Bioinformatics 11-04-2013, 08:32 PM
Replies: 20
Views: 8,990
Posted By jimmybee
Technically thats not really an assembly. TO...

Technically thats not really an assembly.

TO get a consensus sequence, you should look at the variant calling section of the samtools manual (http://samtools.sourceforge.net/mpileup.shtml):
Forum: Bioinformatics 10-31-2013, 03:36 PM
Replies: 17
Views: 3,575
Posted By jimmybee
Do you use chrome by any chance? I had...

Do you use chrome by any chance?

I had similar issues with my system but has since cleared when I switched to safari. Ive been really throttling the system recently and its been handling...
Forum: Bioinformatics 10-27-2013, 04:06 PM
Replies: 17
Views: 3,575
Posted By jimmybee
Ive had no issues

Ive had no issues
Forum: Bioinformatics 10-24-2013, 03:03 PM
Replies: 5
Views: 1,791
Posted By jimmybee
Can you give us an example of what you ran and...

Can you give us an example of what you ran and what you're getting as an output? We can't really help you unless we get some background....
Forum: Bioinformatics 10-24-2013, 03:04 AM
Replies: 7
Views: 2,921
Posted By jimmybee
Just read the instructions on that page: "Due...

Just read the instructions on that page:
"Due spam on the QIIME Forum, we're requiring users to register before posting. As before, viewing the forum does not require registration. We're sorry for...
Forum: Bioinformatics 10-24-2013, 01:51 AM
Replies: 7
Views: 2,921
Posted By jimmybee
May I suggest emailing the Qiime forum...

May I suggest emailing the Qiime forum (https://groups.google.com/forum/#!forum/qiime-forum). They're usually very quick in responding and are probably infinitely more skilled in this subject area
Forum: Bioinformatics 10-19-2013, 04:18 PM
Replies: 1
Views: 1,274
Posted By jimmybee
um do them one at a time samtools view -bS...

um do them one at a time

samtools view -bS -F 4 -o OUTBAM_mapped SAMFILE
samtools view -bS -F 8 -o OUTBAM_unmapped SAMFILE

you can do "samtools merge" to combine them for analysis if thats...
Forum: Bioinformatics 10-08-2013, 02:48 AM
Replies: 1
Views: 1,485
Posted By jimmybee
Maybe try the full path of the file (like what...

Maybe try the full path of the file (like what you did for the input file).
Forum: Bioinformatics 09-19-2013, 03:42 PM
Replies: 6
Views: 2,237
Posted By jimmybee
Yeah no need to modify them.

Yeah no need to modify them.
Forum: Bioinformatics 09-19-2013, 03:18 PM
Replies: 6
Views: 2,237
Posted By jimmybee
No you wont have to map them separately. Create a...

No you wont have to map them separately. Create a multi-fasta file of all your reference sequences and then build the mapping index from that.
Forum: Bioinformatics 09-11-2013, 02:19 PM
Replies: 4
Views: 2,669
Posted By jimmybee
Are you looking to just analyse one gene or a...

Are you looking to just analyse one gene or a gene family? If its one gene then it should be a simple BLAST against scaffold sequences to identify it. If these are unplaced scaffolds that have no...
Forum: Bioinformatics 09-05-2013, 02:48 PM
Replies: 2
Views: 2,429
Posted By jimmybee
It all depends on the genome (complexity,...

It all depends on the genome (complexity, heterozygousity) and the computer resources you have available. Theres no 'one assembler fits this data' you're going to have to have a go at a few and...
Forum: Bioinformatics 09-01-2013, 03:56 PM
Replies: 3
Views: 1,811
Posted By jimmybee
From my experience with mitochondrial and...

From my experience with mitochondrial and chloroplast alignments, Id say less than a week. You could try Clustal-omeg. Im pretty sure its multi-threaded

Your laptop should handle it
Forum: Bioinformatics 08-21-2013, 02:13 AM
Replies: 1
Views: 789
Posted By jimmybee
Im sorry but unless you give us information about...

Im sorry but unless you give us information about what you did, we will have no way of helping you.

What commands did you run? Go through step-by-step. What reference sequence were you using? etc...
Forum: Bioinformatics 08-11-2013, 05:47 PM
Replies: 2
Views: 948
Posted By jimmybee
Yes you are able to override GACT keypass but I...

Yes you are able to override GACT keypass but I know you have to do some significant editing of parameter files to do so. I have done it before, but unfortunately I've lost the information. The best...
Forum: Bioinformatics 08-10-2013, 08:16 PM
Replies: 30
Views: 5,304
Posted By jimmybee
Did a few edits today but will keep adding :)

Did a few edits today but will keep adding :)
Showing results 1 to 25 of 119

 


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