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Forum: Bioinformatics 05-06-2017, 04:07 PM
Replies: 331
Views: 120,243
Posted By Torst
This behaviour is a bit un-Unix like? ...

This behaviour is a bit un-Unix like?


bbduk.sh in1=R1.fq.gz in2=R2.fq.gz loglog loglogk=31 out=/dev/null

Unspecified format for output /dev/null; defaulting to fastq.

Exception in thread...
Forum: Bioinformatics 09-10-2013, 06:21 PM
Replies: 4
Views: 2,728
Posted By Torst
Lightbulb Yes you do. But you can do it all quite easily...

Yes you do. But you can do it all quite easily using the "Generic.tsv" tab separated file you can create with a script or with some Excel wizardry. The online portal allows you to download it, or...
Forum: Bioinformatics 06-07-2013, 04:39 PM
Replies: 5
Views: 1,982
Posted By Torst
FYI - lh3 is the author of bwa-mem, but he seems...

FYI - lh3 is the author of bwa-mem, but he seems to know what he is doing ;-)

I think bwa-mem still focuses on local alignment, but if it can find a glocal alignment that is nearly as good (high...
Forum: Bioinformatics 06-06-2013, 04:16 PM
Replies: 2
Views: 1,575
Posted By Torst
Do you mean $hit->next_hsp instead of $hit->hsp...

Do you mean $hit->next_hsp instead of $hit->hsp ?
Forum: Bioinformatics 06-06-2013, 04:14 PM
Replies: 5
Views: 1,982
Posted By Torst
BWA is a "local" aligner. If you require that the...

BWA is a "local" aligner. If you require that the WHOLE query sequence must be included in the alignment, you need a "glocal" aligner (global in query, local in target). You can use glsearch36 from...
Forum: Bioinformatics 06-06-2013, 03:24 PM
Replies: 3
Views: 2,397
Posted By Torst
No. I only know that list. I've never used any of...

No. I only know that list. I've never used any of them.
Forum: Bioinformatics 06-06-2013, 03:24 PM
Replies: 4
Views: 3,631
Posted By Torst
All the adaptors are in a PDF that you have to...

All the adaptors are in a PDF that you have to ask Illumina for. They recently changed their policy and allow you to dsitribute them in software.

Trimmomatic comes with them now, but you still...
Forum: Bioinformatics 06-06-2013, 03:19 PM
Replies: 13
Views: 1,452
Posted By Torst
Lightbulb BLAST Manual

BLAST Command Line Applications User Manual

http://www.ncbi.nlm.nih.gov/books/NBK1763/
Forum: Bioinformatics 06-06-2013, 01:44 AM
Replies: 3
Views: 2,397
Posted By Torst
It's not an easily solved problem. Most gene...

It's not an easily solved problem. Most gene finders can't even predict the correct start codon site, let alone the promoter. The TSS can be gleaned from RNA-Seq data to some extent.

This web...
Forum: Academic/Non-Profit Jobs 06-06-2013, 01:41 AM
Replies: 1
Views: 3,775
Posted By Torst
If you find > 1 person that matches those...

If you find > 1 person that matches those qualifications, let me know :-)
Forum: Bioinformatics 06-06-2013, 01:38 AM
Replies: 1
Views: 1,583
Posted By Torst
Darren, maybe you should re-post with the lines...

Darren, maybe you should re-post with the lines numbered. You can use the Unix "nl" command to do this.
Forum: RNA Sequencing 06-06-2013, 01:36 AM
Replies: 3
Views: 1,750
Posted By Torst
DNA or RNA? What organism? Fresh, frozen,...

DNA or RNA?
What organism?
Fresh, frozen, FFPE ?
Forum: Bioinformatics 06-06-2013, 01:31 AM
Replies: 2
Views: 5,626
Posted By Torst
If you parse with Bio::Perl, you can use the...

If you parse with Bio::Perl, you can use the tile_hsps() function in the GenericHit module and use the coordinates it provides.
Forum: Bioinformatics 06-06-2013, 01:29 AM
Replies: 1
Views: 1,056
Posted By Torst
Hello from Melbourne. No, read depth is...

Hello from Melbourne.

No, read depth is independent of read length.

Depth will depend on the genome size of the organism you sequenced however. It's the average number of reads that include a...
Forum: Bioinformatics 06-06-2013, 01:23 AM
Replies: 1
Views: 1,093
Posted By Torst
In my experience, yes, the "sampe" step is a...

In my experience, yes, the "sampe" step is a bottleneck, whereas the "aln" step is really fast. Frustrating.

The main problem is disk i/o speed, especially if you are reading from and writing to a...
Forum: Illumina/Solexa 06-06-2013, 01:19 AM
Replies: 2
Views: 2,623
Posted By Torst
Yes this is unfortunately very common. Library...

Yes this is unfortunately very common. Library prep is very sensitive to timings and amounts.

Read about Nick's experiences here:...
Forum: Bioinformatics 06-06-2013, 01:17 AM
Replies: 4
Views: 3,631
Posted By Torst
Did your adapter clipping actually include the...

Did your adapter clipping actually include the new Nextera adaptors?

Notice Nick Loman had similar TTATA in his FASTQC analysis. Your library is too short and you are getting overlapping reads...
Forum: Bioinformatics 06-06-2013, 01:14 AM
Replies: 1
Views: 1,316
Posted By Torst
PHAST(PHAge Search Tool) is a web server designed...

PHAST(PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids.
...
Forum: Bioinformatics 06-06-2013, 01:13 AM
Replies: 1
Views: 696
Posted By Torst
Yes you can! ...

Yes you can!

http://www.ncbi.nlm.nih.gov/pubmed/21677692
Forum: Bioinformatics 06-06-2013, 01:08 AM
Replies: 13
Views: 1,452
Posted By Torst
It is very unlikely that there exists a script to...

It is very unlikely that there exists a script to do what you want!

You will need a bespoke solution. It could probably be done using a series of Unix tools, but ultimately a custom Perl/Python...
Forum: Bioinformatics 06-06-2013, 01:02 AM
Replies: 2
Views: 2,112
Posted By Torst
Lightbulb Looking at the source code shows this: ...

Looking at the source code shows this:

double skew = (double) cMinusG / (double) cPlusG;

Which means it is (probably) using (C-G)/(C+G).
Forum: Bioinformatics 06-05-2013, 11:12 PM
Replies: 44
Views: 30,380
Posted By Torst
Exclamation Yes, according to the manual (PDF) it assumes...

Yes, according to the manual (PDF) it assumes strand-specific reads. If you don't have them, you need to enable an option.
Forum: Bioinformatics 04-17-2013, 04:23 PM
Replies: 17
Views: 3,311
Posted By Torst
The guess of Pseudomonas was based on genome...

The guess of Pseudomonas was based on genome size, number of contigs, and googling your name :-) I had similar results for the Pa AES strains.

Nextera seems to produce a lot of very short reads,...
Forum: Bioinformatics 04-17-2013, 01:48 AM
Replies: 17
Views: 3,311
Posted By Torst
You should run velvetg WITHOUT the two auto...

You should run velvetg WITHOUT the two auto options first if you want to examine the coverage plot in R.

There is no need to set -max_coverage unless you know you have some known HIGH level of...
Forum: Bioinformatics 01-07-2013, 10:08 PM
Replies: 4
Views: 1,510
Posted By Torst
Is this brand new Nextera MATE PAIR or PAIRED END...

Is this brand new Nextera MATE PAIR or PAIRED END protocol reads?

As for overlapping problems, it's a balance of probability guess work:...
Showing results 1 to 25 of 275

 


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