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Forum: Bioinformatics 08-17-2015, 06:06 AM
Replies: 1
Views: 583
Posted By sphil
If I understand correctly you want to reduce your...

If I understand correctly you want to reduce your dimensionality without loosing information (as far as possible). What comes into my mind is that you need some kind of pre clustering using some sort...
Forum: Bioinformatics 03-23-2015, 05:36 AM
Replies: 0
Views: 775
Posted By sphil
antimicrobial resistance frequencies database

Hi there,



does anyone know where I can download a parseable database which contains antibiotic resistance frequencies?

I found this database http://arpcard.mcmaster.ca/ , but this only...
Forum: Bioinformatics 03-12-2015, 05:48 AM
Replies: 3
Views: 1,261
Posted By sphil
Hi, AFAIK fishers exact test tries to answer...

Hi,

AFAIK fishers exact test tries to answer for independence between the two variables. First, I don't think this is what you want to test for (am I right?). Second, i think your groups are not...
Forum: Bioinformatics 03-06-2015, 12:42 AM
Replies: 5
Views: 2,669
Posted By sphil
you can use QIIME (even though it is on your own...

you can use QIIME (even though it is on your own risk, as they state)

http://qiime.org/tutorials/shotgun_analysis.html
Forum: Bioinformatics 09-11-2014, 12:32 AM
Replies: 42
Views: 6,406
Posted By sphil
That you can't use more cores might have...

That you can't use more cores might have something to do with the setup of your virtual machine. If you only hand through one core, it is obvious that you can't work with 8.... Check on that if you...
Forum: Bioinformatics 08-27-2014, 06:40 AM
Replies: 4
Views: 1,576
Posted By sphil
can't this be done by basically every mapper...

can't this be done by basically every mapper which output bam/sam and is aware finding exon junctions?
Forum: Bioinformatics 07-15-2014, 01:30 AM
Replies: 0
Views: 2,024
Posted By sphil
rarefaction curves and simulation

Hiho

i want to create a rarefaction curve using R i.e. vegan {rearecurve/speccaccum}.

This worked out quite well (please see here (http://imgur.com/7gPo7gv))

Anyways, as you can see in the...
Forum: Bioinformatics 07-14-2014, 11:26 PM
Replies: 4
Views: 1,655
Posted By sphil
from bowtie manual: Alignment summmary ...

from bowtie manual:
Alignment summmary

When Bowtie 2 finishes running, it prints messages summarizing what happened. These messages are printed to the "standard error" ("stderr") filehandle. For...
Forum: Bioinformatics 07-04-2014, 01:46 AM
Replies: 2
Views: 1,188
Posted By sphil
check out mira...

check out mira (http://mira-assembler.sourceforge.net/) , or maybe mauve (http://gel.ahabs.wisc.edu/mauve/)
Forum: Bioinformatics 05-06-2014, 12:08 AM
Replies: 2
Views: 1,519
Posted By sphil
When you are using a HiSeq2500, can't you also go...

When you are using a HiSeq2500, can't you also go with 2x150 (Rapid mode?). Either way, imho it depends on for what kind of organism you are trying to identify the transcriptome. Rather complex one...
Forum: Bioinformatics 04-22-2014, 10:24 PM
Replies: 6
Views: 2,957
Posted By sphil
wow, long time no see ;) Actually I can't...

wow, long time no see ;)
Actually I can't remember but I guess i worked my way through their tutorial....
Forum: Bioinformatics 04-01-2014, 08:36 AM
Replies: 9
Views: 4,493
Posted By sphil
I acutally don't see any problem with that....

I acutally don't see any problem with that. However, I actually have no clue how much sequence similarity there is between those MT-Genomes. But anyways I would definitely give it a try!!!
Forum: Bioinformatics 04-01-2014, 01:13 AM
Replies: 2
Views: 1,813
Posted By sphil
Why would you only be able to use 2 isoforms? You...

Why would you only be able to use 2 isoforms? You might declare one as the 'standard isoform' which is ok doing by random since you will always use this isoform. Calculate every ratio of interest...
Forum: Bioinformatics 04-01-2014, 01:08 AM
Replies: 7
Views: 1,960
Posted By sphil
look at the 'INSTALL' but normally things go...

look at the 'INSTALL' but normally things go like:

./configure
make
make install (you may need 'su' priviledges for that)...
Forum: Bioinformatics 04-01-2014, 01:06 AM
Replies: 9
Views: 4,493
Posted By sphil
Since MT-Genomes aren't that large, imo he could...

Since MT-Genomes aren't that large, imo he could also 'cat' all MTgenomes.fa he wants to into one genome. Map against this, since the mapping location will give rise to which genome the reads map you...
Forum: Bioinformatics 04-01-2014, 01:01 AM
Replies: 8
Views: 1,799
Posted By sphil
what do you mean by "compare"? I doubt that...

what do you mean by "compare"? I doubt that mappers like BWA.. are capable of doing this. They are desinged to work with short sequences, <120bp, so they won't compare sequences of, approx. 1kb, very...
Forum: Bioinformatics 04-01-2014, 12:56 AM
Replies: 2
Views: 980
Posted By sphil
To force blast to only output uniq alignments is,...

To force blast to only output uniq alignments is, AFAIK, not possible. If you want to gain only the 'uniqe' ones you have to filter after retrieving the results.
Forum: Bioinformatics 03-21-2014, 06:09 AM
Replies: 6
Views: 2,633
Posted By sphil
doesn't --un-con and --al-conc just state wether...

doesn't --un-con and --al-conc just state wether pairs could be mapped concordantly and not whether they could be mapped at all?
Forum: Metagenomics 03-13-2014, 07:17 AM
Replies: 1
Views: 1,346
Posted By sphil
create a gff with your genes your just found...

create a gff with your genes your just found denovo. then, you can use almost every software for quantification since you got the genome (your contigs) and the genes..
Forum: Metagenomics 03-13-2014, 07:15 AM
Replies: 2
Views: 3,124
Posted By sphil
have a look at the program FLASH...

have a look at the program FLASH (http://ccb.jhu.edu/software/FLASH/), it might help! It does good work and especially for your task, try to use it after your first initial assembly...
Forum: Bioinformatics 02-10-2014, 05:50 AM
Replies: 5
Views: 1,632
Posted By sphil
DESeq and all other DE software like edreR... are...

DESeq and all other DE software like edreR... are not capable of calculating DE-Genes w/o replicates. In fact you can't (of course you can force them but...) use this kind of software for that. Your...
Forum: Bioinformatics 02-10-2014, 05:43 AM
Replies: 5
Views: 1,417
Posted By sphil
Nope it is not. Ask your sequencing...

Nope it is not.


Ask your sequencing center to provide the sequences than you can look for it.
Forum: Bioinformatics 02-10-2014, 05:42 AM
Replies: 3
Views: 1,568
Posted By sphil
you could pull the readnames of interest from you...

you could pull the readnames of interest from you sam/bam file using samtools. Use those names to grep for the sequences in your fastq and check how the qualities are.
Forum: Bioinformatics 02-06-2014, 03:03 AM
Replies: 16
Views: 6,877
Posted By sphil
Why should it use all memory? It can only handle...

Why should it use all memory? It can only handle as many reads at the same time as you have CPU-kernels on hand. This should then somehow correlate with the memory used....
Forum: Bioinformatics 02-06-2014, 02:05 AM
Replies: 16
Views: 6,877
Posted By sphil
What comes into my mind is that every of your 10k...

What comes into my mind is that every of your 10k sequences might end up aligning to a huge amount of sequences in the NR database. Therefore the output file is also very large (maybe compare...)....
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