SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 137
Search took 0.04 seconds.
Search: Posts Made By: sarvidsson
Forum: De novo discovery 03-25-2015, 05:41 AM
Replies: 4
Views: 1,766
Posted By sarvidsson
Yes, you'll get (possibly much) larger contigs -...

Yes, you'll get (possibly much) larger contigs - at least if you can make an appropriately sized library (you'd want 400-700 inserts).



With Illumina-only data, you'd need long-insert (3 kb or...
Forum: RNA Sequencing 03-23-2015, 02:08 AM
Replies: 4
Views: 1,514
Posted By sarvidsson
The --input (or -i) argument is the format, not...

The --input (or -i) argument is the format, not the actual input file. It expects input on stdin, which you can pass by using the "<" operator.
Forum: RNA Sequencing 03-23-2015, 02:04 AM
Replies: 6
Views: 1,051
Posted By sarvidsson
Try convert2bed -i SAM < 1.sam > 1.bed

Try convert2bed -i SAM < 1.sam > 1.bed
Forum: Bioinformatics 03-20-2015, 12:49 AM
Replies: 3
Views: 1,485
Posted By sarvidsson
Your library preparation does not preserve strand...

Your library preparation does not preserve strand information, so the sequences in your FASTQ files randomly correspond to either the original strand of the mRNA or the reverse complement of it. So...
Forum: Metagenomics 03-19-2015, 06:10 AM
Replies: 7
Views: 1,747
Posted By sarvidsson
MetaVelvet and SPAdes would typically need much...

MetaVelvet and SPAdes would typically need much more than 24 GB RAM, something like >= 128 GB would be appropriate.
Forum: Bioinformatics 03-17-2015, 02:22 AM
Replies: 8
Views: 1,233
Posted By sarvidsson
96 GB can be a bit tight, 24 cores should be fine...

96 GB can be a bit tight, 24 cores should be fine - I'd expect the assembly to run for up to 3 days. If you error correct and normalize the paired end reads prior to assembly (with e.g. BBNorm...
Forum: Bioinformatics 03-17-2015, 01:52 AM
Replies: 8
Views: 1,233
Posted By sarvidsson
I'd try Allpaths-LG...

I'd try Allpaths-LG (http://www.broadinstitute.org/software/allpaths-lg/blog/) if your paired end reads mostly overlap (i.e. fragment size of ~180 bp). It will use your mate pairs for scaffolding.
Forum: Bioinformatics 03-13-2015, 01:06 AM
Replies: 17
Views: 3,973
Posted By sarvidsson
It could also be rRNA; what does the GC plot (per...

It could also be rRNA; what does the GC plot (per sequence GC content) look like?
Forum: Bioinformatics 03-12-2015, 08:24 AM
Replies: 9
Views: 2,104
Posted By sarvidsson
You don't need to load the whole thing in R for...

You don't need to load the whole thing in R for that,


cut -f 3,4 in.vcf | grep '\-$' | cut -f 1 > ref_dash_ID-list
cut -f 3,5 in.vcf | grep '\-$' | cut -f 1 > alt_dash_ID-list


would be...
Forum: Bioinformatics 03-12-2015, 08:12 AM
Replies: 9
Views: 2,104
Posted By sarvidsson
Exactly. I'd check with the TASSEL people that...

Exactly. I'd check with the TASSEL people that those records are really indels, perhaps they can fix the VCF output for a future version.
Forum: Bioinformatics 03-12-2015, 08:09 AM
Replies: 9
Views: 2,104
Posted By sarvidsson
A quick and dirty way to filter these files would...

A quick and dirty way to filter these files would be to

grep -v $'\t-\t' in.vcf > no_indels.vcf

in case there are no other tab-separated fields with dashes. Check that with:

grep $'\t-\t'...
Forum: Bioinformatics 03-12-2015, 08:02 AM
Replies: 9
Views: 2,104
Posted By sarvidsson
Then their conformity is broken:...

Then their conformity is broken: http://www.1000genomes.org/node/101; the allowed contents of the REF and ALT fields are the same for 4.0 as 4.1.
Forum: Bioinformatics 03-12-2015, 07:54 AM
Replies: 9
Views: 2,104
Posted By sarvidsson
What VCF version should that be (and what...

What VCF version should that be (and what software called those)? It is not proper VCF4.1 or 4.2 - dashes are not allowed as bases, so no wonder that the tools you tried couldn't identify those as...
Forum: Bioinformatics 03-02-2015, 05:38 AM
Replies: 4
Views: 1,449
Posted By sarvidsson
Try vcf-annotate in VCFtools...

Try vcf-annotate in VCFtools http://vcftools.sourceforge.net/perl_module.html#vcf-annotate - look under "read even more" to get examples on how to create custom filters for DP4.
Forum: Bioinformatics 03-02-2015, 05:23 AM
Replies: 5
Views: 644
Posted By sarvidsson
Basically correct, with the following extension: ...

Basically correct, with the following extension:

1/1 is homozygous for allele 1 (parent 1, if parent 1 contained the first allele listed in ALT)
2/2 is homozygous for allele 2 (parent 2, if...
Forum: Bioinformatics 03-02-2015, 03:40 AM
Replies: 8
Views: 849
Posted By sarvidsson
You can make your own pairwise comparisons - but...

You can make your own pairwise comparisons - but you need the standalone version (bottom of the page).
Forum: Bioinformatics 03-02-2015, 02:02 AM
Replies: 8
Views: 849
Posted By sarvidsson
See the edited post ;)

See the edited post ;)
Forum: Bioinformatics 03-02-2015, 01:54 AM
Replies: 8
Views: 849
Posted By sarvidsson
Sorry, overlooked that you were talking about...

Sorry, overlooked that you were talking about transcriptomes. For transcontigs, standalone InParanoid (http://inparanoid.sbc.su.se/cgi-bin/index.cgi) is worth a try - limited to protein coding...
Forum: Bioinformatics 03-02-2015, 01:33 AM
Replies: 9
Views: 1,750
Posted By sarvidsson
There is no simple solution to variant calling...

There is no simple solution to variant calling and genotyping in low-coverage loci using RNA-Seq data - shotgun DNA and a proper multi-sample caller would give you much more robust data.

You...
Forum: Bioinformatics 02-27-2015, 07:43 AM
Replies: 9
Views: 1,750
Posted By sarvidsson
Just a question from the technical/analytical...

Just a question from the technical/analytical side (I like to check the technical things before going to deep into biological reasoning): Did you look at the quality of the data underlying the calls...
Forum: Bioinformatics 02-26-2015, 12:23 AM
Replies: 2
Views: 606
Posted By sarvidsson
Not familiar with the exact format VEP outputs,...

Not familiar with the exact format VEP outputs, could you post a couple of data lines from it? I'd assume that it simply adds a INFO field tag, which could be removed by sed.
Forum: Bioinformatics 02-26-2015, 12:20 AM
Replies: 18
Views: 4,301
Posted By sarvidsson
I'll have a look at the custom workflows. Would...

I'll have a look at the custom workflows. Would it be possible to bulk import thousands of (typically paired) FASTQ files and assigning sample IDs to them?



VCF would be nice but is not a...
Forum: Bioinformatics 02-26-2015, 12:11 AM
Replies: 5
Views: 1,097
Posted By sarvidsson
Then you are rather limited in what you can do -...

Then you are rather limited in what you can do - looking at the data qualitatively as nucacidhunter suggested might be possible, but be careful in determining "culture only" expressed genes with low...
Forum: RNA Sequencing 02-26-2015, 12:03 AM
Replies: 9
Views: 2,264
Posted By sarvidsson
The library costs tend to be prohibitive for the...

The library costs tend to be prohibitive for the academic customers we have - from 454 to Illumina these costs haven't dropped by far as much as the sequencing costs have. So a "screen few samples...
Forum: Bioinformatics 02-25-2015, 02:46 AM
Replies: 18
Views: 4,301
Posted By sarvidsson
One of my colleagues has a Geneious license, so I...

One of my colleagues has a Geneious license, so I might try it. However, I'm a command line guy - is there a way to automate Geneious for amplicon data? (I typically have thousands of samples with...
Showing results 1 to 25 of 137

 


All times are GMT -8. The time now is 07:29 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO