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Search: Posts Made By: Kasycas
Forum: Genomic Resequencing 04-05-2012, 07:08 AM
Replies: 27
Views: 16,689
Posted By Kasycas
Yep, got that alright. Position just isn't enough...

Yep, got that alright. Position just isn't enough because you then need to see the gene's it's affecting. I guess it means writing a script.

Thanks for your response anyway, it's always better...
Forum: Genomic Resequencing 04-05-2012, 06:38 AM
Replies: 27
Views: 16,689
Posted By Kasycas
@jgibbons1 Both actually, it would be nice...

@jgibbons1

Both actually, it would be nice to have interpretable output where you can see how relevant a particular SNP is. Therefore, I was trying to get information such as; what gene it's from,...
Forum: Genomic Resequencing 04-05-2012, 12:30 AM
Replies: 27
Views: 16,689
Posted By Kasycas
Hi jgibbons1, I've been using MAQ as well but the...

Hi jgibbons1, I've been using MAQ as well but the snp output is useless without annotation. Have you come across a good way to annotate the output that MAQ produces?

Thanks!
Forum: Bioinformatics 04-03-2012, 08:15 AM
Replies: 5
Views: 3,429
Posted By Kasycas
I have the same problem -- == statmap report...

I have the same problem

-- == statmap report ==

-- # single end (SE) reads: 0
-- # mapped SE reads: 0 (/ 0 = NA%)
-- # paired end (PE) reads: 30130376
-- # mapped PE reads: 28705774 (/...
Forum: Bioinformatics 03-26-2012, 05:13 AM
Replies: 2
Views: 4,112
Posted By Kasycas
Dear natstreet, I'm currently wondering if...

Dear natstreet,

I'm currently wondering if this is a problem I'm having as my mate pair Illumina data is not assembling as all with Velvet, although soapdenovo seems to be working ok. Why would...
Forum: Bioinformatics 02-28-2012, 01:33 AM
Replies: 3
Views: 2,666
Posted By Kasycas
Back on this topic, is GATK ok to use for the...

Back on this topic, is GATK ok to use for the detection of prokaryotic SNPs with Illumina data? A lot of the information I'm reading refers to human data so I'm just worried I'd use it incorrectly. ...
Forum: Bioinformatics 07-21-2011, 01:26 PM
Replies: 3
Views: 1,551
Posted By Kasycas
Thanks for the answers vadim and maubp, I'll give...

Thanks for the answers vadim and maubp, I'll give them a go. I hadn't realised Roche had this sfffile tool and Galaxy's a good option as well.
Forum: Bioinformatics 07-15-2011, 01:48 AM
Replies: 3
Views: 1,551
Posted By Kasycas
extracted sequences from sff

Hi,

Has anyone successfully extracted a subset of sequences by their read ID from an sff file? I'm trying to separate plasmid and chromosomal reads from a bacterial sequencing project and I've...
Forum: De novo discovery 03-07-2011, 03:38 AM
Replies: 3
Views: 4,290
Posted By Kasycas
Coverage required for SNP detection?

Hi all,

I am sequencing bacterial genomes, certain genomic strains of which have been published but not the exact strains I'll be trying to detect SNPs for.

First off, as my title asks, can...
Forum: Bioinformatics 02-21-2011, 08:28 AM
Replies: 4
Views: 2,088
Posted By Kasycas
Was it shotgun or paired end/mate pair reads?...

Was it shotgun or paired end/mate pair reads? I've found that 8kb mate pair data on my 4.5Mb bacterial genome works wonders (5 scaffolds). This was done on a 1/4 plate.

Is your organism 7.5Mb and...
Forum: Bioinformatics 02-21-2011, 03:11 AM
Replies: 3
Views: 2,666
Posted By Kasycas
Thanks Nickloman. I hadn't used this part of...

Thanks Nickloman. I hadn't used this part of Newbler before. I'll check it out.
Forum: Bioinformatics 02-21-2011, 02:21 AM
Replies: 3
Views: 2,666
Posted By Kasycas
calling SNPs for prokaryotes

Hi,

I have genomic prokaryotic data and I want to look at SNPs between my data and the existing published data for very similar species. However, where MAQ worked well previously with Illumina...
Forum: Bioinformatics 11-15-2010, 04:20 AM
Replies: 11
Views: 12,001
Posted By Kasycas
Hi SH1, I am also interested in your...

Hi SH1,

I am also interested in your question. Have you found out?!

Thanks,

Kasycas
Forum: Bioinformatics 09-10-2010, 02:52 AM
Replies: 1
Views: 2,579
Posted By Kasycas
MIRA output for Illumina mapping giving 100% coverage!

Hi all,

I've been using MIRA as I have both Illumina and 454 reads that I wanted to do mapping/assembly as well as semi-hybrid and hybrid assembly. However, when I use MIRA on the Illumina data...
Forum: Bioinformatics 06-14-2010, 05:59 AM
Replies: 8
Views: 3,568
Posted By Kasycas
Hi niazi84@hotmail.com, Did you find out...

Hi niazi84@hotmail.com,

Did you find out about this reference file? I can't find much info anywhere about it!

Thanks,

Kasycas
Forum: RNA Sequencing 04-26-2010, 12:40 PM
Replies: 25
Views: 12,027
Posted By Kasycas
further issues

Dear all,

I'm still having a great deal of trouble with ERANGE. Whether I use paired end data or single read, I get the following error on the very last script of the runStandardAnalysis.sh...
Forum: Bioinformatics 02-22-2010, 08:33 AM
Replies: 47
Views: 29,437
Posted By Kasycas
One more thing on a slightly separate issue. The...

One more thing on a slightly separate issue. The output from cuffcompare stdout.tracking, according to the manual should contain;

Each of the columns after the fifth have the following format:
...
Forum: Bioinformatics 02-22-2010, 02:48 AM
Replies: 47
Views: 29,437
Posted By Kasycas
Hi Cole, Thanks for the new release! I've...

Hi Cole,

Thanks for the new release! I've been trying to use cuffdiff as described above. It runs for a while and then terminates as follows;

Importance sampling posterior distribution...
Forum: RNA Sequencing 12-21-2009, 02:36 AM
Replies: 25
Views: 12,027
Posted By Kasycas
Hi, I have a traceback error as well but...

Hi,

I have a traceback error as well but it's not related to Cistematic.

python geneMrnaCountsWeighted.py human bowtie_1205_2_hg18.rds bowtie_1205_2_hg18.expanded.rpkm...
Forum: Bioinformatics 11-30-2009, 06:37 AM
Replies: 3
Views: 2,466
Posted By Kasycas
same problem

Hi,

I have the same problem. Did Leo's solution work for you dukevn?

Thanks!
Forum: RNA Sequencing 11-24-2009, 03:17 AM
Replies: 9
Views: 4,740
Posted By Kasycas
spike sequences

Hi,

I am also wondering about the OP's question about spike sequences. They seem to be mentioned only in the ERANGE paper and online help files with no mention of what they actually are! Any...
Forum: Bioinformatics 11-17-2009, 12:42 AM
Replies: 11
Views: 4,898
Posted By Kasycas
same problem

Hi,

Was this problem resolved? I have a similar issue where I had 2 input files and the current ensembl reference genome (Homo_sapiens.GRCh37.56.gtf) but no references mapped and I only got 1...
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