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Forum: Bioinformatics 01-09-2018, 07:46 AM
Replies: 0
Views: 286
Posted By TabeaK
Geneset/Signature enrichment summary score

Forgive my lack of knowledge concerning gene sets and signatures, but I am trying to do (and educate myself on) the following:

I have various gene expression datasets (I have both normalized...
Forum: Bioinformatics 07-31-2013, 03:19 AM
Replies: 5
Views: 3,229
Posted By TabeaK
Indeed, using the -outfmt paramater, you can add...

Indeed, using the -outfmt paramater, you can add all of the fields specified in the manual, see here from the manual:

outfmt string 0

alignment view options:
0 = pairwise,
1 = query-anchored...
Forum: Bioinformatics 07-29-2013, 11:20 AM
Replies: 5
Views: 3,229
Posted By TabeaK
Nevermind...:eek::D User error. I managed to mess...

Nevermind...:eek::D User error. I managed to mess up the columns while filtering the blast result...
Forum: Bioinformatics 07-29-2013, 10:46 AM
Replies: 5
Views: 3,229
Posted By TabeaK
blastn - qcovs field - or how to parse results based on % coverage of query sequence

I have been playing around with blast+ (blastn), a local installation and various custom databases.

I thought I had my workflow figured out, but some output is confusing me.

Specifically the...
Forum: Bioinformatics 07-29-2013, 10:36 AM
Replies: 3
Views: 959
Posted By TabeaK
I've been doing something similar recently -...

I've been doing something similar recently - mainly via awk command from a tabbed blast+ output and then using this file to filter an input sequence file.

If you elaborate a little on what you are...
Forum: Bioinformatics 07-18-2013, 03:43 PM
Replies: 2
Views: 784
Posted By TabeaK
Cheers, I'll play around with this a little!

Cheers, I'll play around with this a little!
Forum: Bioinformatics 07-18-2013, 04:55 AM
Replies: 2
Views: 784
Posted By TabeaK
Alignment & visualisation of two similar contigs

Hi guys!

I am currently trying to figure out how to compare two or more similar contigs on a global scale. I have my reference contig and a selection of corresponding contigs from other strains....
Forum: Bioinformatics 03-14-2013, 02:35 PM
Replies: 1
Views: 1,105
Posted By TabeaK
qseq to fastq - post conversion quality trimming

Hiya!

I have a bunch of old RNAseq data sets that I want to re-analyse using our current pipeline. First challenge was that the data is old enough to have been archived in qseq format, not fastq....
Forum: Bioinformatics 01-07-2013, 08:33 AM
Replies: 3
Views: 1,084
Posted By TabeaK
Okay, problem solved... This little thing: ...

Okay, problem solved...

This little thing:

11.2 Parsing NCBI fasta files

NCBI fasta files use a >gi|nnn|ref|xxx identifier. By default
Stampy parses this and uses only the "xxx" part. ...
Forum: Bioinformatics 01-07-2013, 06:04 AM
Replies: 3
Views: 1,084
Posted By TabeaK
Ha! :) I think this is the problem:...

Ha! :) I think this is the problem: http://seqanswers.com/forums/showthread.php?t=17486

I also get only 'N' in the ref column...no I just need to figure out what the hell is going on.
Forum: Bioinformatics 01-07-2013, 12:08 AM
Replies: 3
Views: 1,084
Posted By TabeaK
Bumpety-bump. :)

Bumpety-bump. :)
Forum: Bioinformatics 01-04-2013, 08:59 AM
Replies: 3
Views: 1,084
Posted By TabeaK
Samtools mpileup - why does it call an "N" when there ARE correct alignments?

Hi all!

Happy 2013! :)

I am having a bit of an issue with generating consensus sequences from an Alignment BAM file.

The alignment was done with Stampy. It is a mix of single end and paired...
Forum: Bioinformatics 12-13-2012, 02:43 AM
Replies: 5
Views: 902
Posted By TabeaK
So; you have a lot of reads; but no reference...

So; you have a lot of reads; but no reference genome? Sounds like classical assembly to me.

What organism are you working on?
Forum: Bioinformatics 12-12-2012, 10:27 AM
Replies: 5
Views: 902
Posted By TabeaK
I am not sure I understand you. So you do not...

I am not sure I understand you. So you do not have a reference sequence?

That would mean you have to assemble one first. Which means you are looking for an assembly tool; not an alignment tool.
Forum: Bioinformatics 12-12-2012, 10:18 AM
Replies: 33
Views: 6,224
Posted By TabeaK
I realise I never got back on this thread: I have...

I realise I never got back on this thread: I have also not had any decent alignments using BWA 0.6.x. I since downgraded to 0.5.x and everything is running well.
Forum: Bioinformatics 12-12-2012, 10:15 AM
Replies: 2
Views: 826
Posted By TabeaK
If I am not mistaken (been a while since I...

If I am not mistaken (been a while since I installed BWA); you have to compile it first.

Try typing make while being in the bwa directory.

And if you are working on mac; you may wanna read...
Forum: Bioinformatics 12-12-2012, 08:37 AM
Replies: 4
Views: 1,412
Posted By TabeaK
:) Some progress. Apologies if it seems...

:) Some progress.

Apologies if it seems like I am talking to myself; but maybe at some point someone will search for the same issue and this may help...;)

So; after using the vcfutils and f2q...
Forum: Bioinformatics 12-12-2012, 08:25 AM
Replies: 4
Views: 1,412
Posted By TabeaK
Thanks for the offer! I'll email you a bit of...

Thanks for the offer! I'll email you a bit of data from both fasta and gff ASAP.
Forum: Bioinformatics 12-12-2012, 07:26 AM
Replies: 4
Views: 1,412
Posted By TabeaK
Ho Jim; thanks for your answer! I am running...

Ho Jim; thanks for your answer!

I am running version 2.1.28 on MacOSX 7.4.

Working brilliantly (great tool!); apart from viewing annotations.

I'll try your suggestion and report back.
Forum: Bioinformatics 12-11-2012, 01:44 PM
Replies: 4
Views: 1,412
Posted By TabeaK
Okay: after a lot of reading around here on...

Okay: after a lot of reading around here on seqanswers, I think I have managed to some of this with samtools - always helps to read the manual carefully. :D

Only thing where I am stuck is the...
Forum: Bioinformatics 12-11-2012, 08:58 AM
Replies: 4
Views: 1,412
Posted By TabeaK
Advice on tools sought - exporting consensus sequences with coverage & SNPs?

Hi all!

I need some tools advice. :)
So; I have mapped reads in BAM format.
I have called SNPs using samtools/bcftools.

Are there any good tools for exporting consensus sequences from; say a...
Forum: Bioinformatics 12-11-2012, 07:49 AM
Replies: 4
Views: 1,412
Posted By TabeaK
Annotation viewing in IGV/Tablet - how to create an alias file

Hello everyone!

The problem of the day that has me a little stymied is the following:

I try to visualise a large alignment (bam file) in either IGV or tablet.

I have tried to upload the...
Forum: Bioinformatics 11-30-2012, 02:55 AM
Replies: 5
Views: 1,513
Posted By TabeaK
Okay. That does not necessarily mean that you did...

Okay. That does not necessarily mean that you did anything wrong with stampy - your command looks fine to me (though I am far from being an expert...:)).

It seems; samtools has a problem with the...
Forum: Bioinformatics 11-30-2012, 02:08 AM
Replies: 5
Views: 1,513
Posted By TabeaK
Um, how do yout know it is not recognized as a...

Um, how do yout know it is not recognized as a SAM?
Forum: Bioinformatics 11-29-2012, 01:17 PM
Replies: 2
Views: 1,230
Posted By TabeaK
OMG! :eek: Of course! That is such a simple...

OMG! :eek: Of course! That is such a simple thing...I need to go to bed. :)

Thank you so much maubp! :) Enclosing the entire scaffold name in "" worked like a charm!
Showing results 1 to 25 of 48

 


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