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Forum: RNA Sequencing 04-29-2013, 09:46 AM
Replies: 2
Views: 1,607
Posted By BaCh
Ah, but indeed one expects to have very little...

Ah, but indeed one expects to have very little bacterial content in blood as this tends to be a rather unhealthy situation for patients. However - to stay with the thought experiment from above - if...
Forum: RNA Sequencing 04-29-2013, 01:42 AM
Replies: 2
Views: 1,607
Posted By BaCh
Metagenomic eukaryote/prokaryote RNASeq: ratio of counts to be expected?

Dear all,

I'm going to do RNASeq on a eukaryote including the prokaryotes which populate it (skin, digestive tract etc.). I am wondering about the numbers of transcripts one has to expect coming...
Forum: Bioinformatics 03-26-2012, 03:08 AM
Replies: 1
Views: 2,689
Posted By BaCh
Answer is here:...

Answer is here: http://www.freelists.org/post/mira_talk/how-to-interpret-MIRA-result,1
Forum: Bioinformatics 12-01-2011, 03:26 AM
Replies: 12
Views: 21,361
Posted By BaCh
"sff_extract -Q" seems easier in handling :-) ...

"sff_extract -Q" seems easier in handling :-)

B.
Forum: Bioinformatics 12-01-2011, 02:18 AM
Replies: 6
Views: 3,900
Posted By BaCh
Yes ... oh yes. Has cost me weeks of time and...

Yes ... oh yes. Has cost me weeks of time and lots of nerves. I'll look for ECC on my next development machine.

Here's an account of what happened:
...
Forum: Bioinformatics 11-11-2011, 03:24 AM
Replies: 3
Views: 2,823
Posted By BaCh
Make that ...

Make that

@EAS139:136:FC706VJ:2:2104:15343:197393/1

See also http://en.wikipedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers

B
Forum: Bioinformatics 11-10-2011, 01:02 AM
Replies: 6
Views: 2,239
Posted By BaCh
That restriction is about to fall in the next...

That restriction is about to fall in the next development release of MIRA.

B.
Forum: Bioinformatics 10-26-2011, 11:28 AM
Replies: 7
Views: 2,519
Posted By BaCh
Having the XML is the best thing, but as long as...

Having the XML is the best thing, but as long as the sequence data has "clippings" via lowercase/uppercase, MIRA will understand that. Just turn off the MIRA warning that it wants the XML.

B.
Forum: Bioinformatics 10-26-2011, 12:25 AM
Replies: 7
Views: 2,519
Posted By BaCh
Is there any special reason you want to go the...

Is there any special reason you want to go the sff_extract way instead of directly using the FASTQ files from the SRA?
Forum: Bioinformatics 10-10-2011, 12:57 AM
Replies: 1
Views: 1,848
Posted By BaCh
You cannot immediately duplicate a whole contig...

You cannot immediately duplicate a whole contig as this would also duplicate all reads contained within ... and duplicate read names is something which will break MIRA, gap4, gap5 etc.

Two...
Forum: Bioinformatics 10-06-2011, 03:20 AM
Replies: 3
Views: 2,610
Posted By BaCh
If the genome you are mapping to is a bacterium...

If the genome you are mapping to is a bacterium or lower eukaryote (30 to 100 MB), give MIRA a try. I wrote the mapping routines to behave consistently for exactly these cases.

B.
Forum: Bioinformatics 05-20-2011, 01:25 AM
Replies: 13
Views: 10,081
Posted By BaCh
Oh. My. God. Noooo! No mitochondria or...

Oh. My. God. Noooo! No mitochondria or chloroplasts.

Include mitochondrial and chloroplast data only if you feel sadistic and want to see assembly programs (and then evaluators) sweat: host...
Forum: Bioinformatics 05-19-2011, 12:46 AM
Replies: 13
Views: 10,081
Posted By BaCh
How about adding some smaller genomes? Like one...

How about adding some smaller genomes? Like one or two bacteria and one or two small eukaryotes (yeasts, fungi).

There is a definitive bias from the organizers of both the Assemblathon and dnGASP...
Forum: De novo discovery 05-18-2011, 04:46 AM
Replies: 2
Views: 3,214
Posted By BaCh
I suspect we're talking about EST / RNASeq reads...

I suspect we're talking about EST / RNASeq reads here, right?

If so: MIRA has own routines to clip sequences, and as with other assemblers, you should be very careful not to trim your data set...
Forum: General 05-17-2011, 01:14 AM
Replies: 37
Views: 19,374
Posted By BaCh
I'll second that. At the moment, no single...

I'll second that. At the moment, no single technology is free of flaws. By combining two of them, you get rid of almost all problems. 454 and Illumina happen to be the cheapest solution at the moment...
Forum: Bioinformatics 03-07-2011, 12:21 AM
Replies: 24
Views: 6,987
Posted By BaCh
You are comparing apples and oranges there. ...

You are comparing apples and oranges there.

On the one hand: what you pay for on the bigger servers is the ability to have, e.g., anything between 1 and 8 CPUs with anthing between 2 and 8 cores...
Forum: Bioinformatics 03-05-2011, 07:27 AM
Replies: 24
Views: 6,987
Posted By BaCh
Which does not come in exactly cheap either. The...

Which does not come in exactly cheap either. The biggest instance Amazon currently has to offer is ~68 GiB and will hurt you at USD 2.28 per hour. An own computer with that much memory can be had for...
Forum: Bioinformatics 03-05-2011, 12:43 AM
Replies: 7
Views: 4,977
Posted By BaCh
*cough* 750k times the same gene? I would not...

*cough* 750k times the same gene? I would not expect any program to really assemble that de-novo if not specially primed. In mapping too, the coverage might be somewhat on the unexpected side.

B.
Forum: Bioinformatics 03-04-2011, 05:07 AM
Replies: 4
Views: 2,984
Posted By BaCh
Funny thing is: it was just one sample....

Funny thing is: it was just one sample. Paired-end, but definitively just one sample in one lane. I suspect they took the wrong pre-processing pipeline then.

Thank you very much,
Bastien
Forum: De novo discovery 03-04-2011, 05:04 AM
Replies: 9
Views: 2,422
Posted By BaCh
Errrrrmmmmm ... you do not want to use 36 mers...

Errrrrmmmmm ... you do not want to use 36 mers for de-novo, this will be a total disaster, a cataclysm, a disaster, the apocalypse. At least if you expect to have somewhat presentable genome data.
...
Forum: Bioinformatics 03-04-2011, 04:57 AM
Replies: 4
Views: 2,984
Posted By BaCh
Illumina read naming

Hi,

I recently got a file with Illumina data where the reads are named like this:

HWI-ST525_0039_8_1_3566_2216#GACCAC/1
HWI-ST525_0039_8_1_3673_2244#ACTTGG/1...
Forum: Bioinformatics 03-04-2011, 04:43 AM
Replies: 7
Views: 4,977
Posted By BaCh
I use the current development version of MIRA...

I use the current development version of MIRA (V3.2.1.8) and just went through a RNASeq denovo 100bp with 22m reads.



It is. I regularly use MIRA for genome de-novo with 454 and Illumina...
Forum: Bioinformatics 02-23-2011, 01:08 AM
Replies: 34
Views: 10,975
Posted By BaCh
Starting with the next stable version of MIRA,...

Starting with the next stable version of MIRA, OSX binaries provided should run on any OSX >=10.5. Furthermore, compiling the sources yourself should be way more easy on OSX (almost as easy as on...
Forum: Bioinformatics 02-23-2011, 01:02 AM
Replies: 8
Views: 2,700
Posted By BaCh
He is, though more easily reachable via the MIRA...

He is, though more easily reachable via the MIRA talk mailing list ... I unfortunately do not have enough time nowadays to scan SEQanswers everyday :(

B.
Forum: Bioinformatics 12-01-2010, 03:49 AM
Replies: 16
Views: 5,234
Posted By BaCh
You sure about that ".com" ending? My...

You sure about that ".com" ending?

My company filter blocked me saying it was a gambling site. A quick search on Google gave www.hgvs.org as most probable address.

B.
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