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Forum: Bioinformatics 11-23-2016, 03:35 AM
Replies: 5
Views: 2,117
Posted By rhinoceros
AFAIK, Bio-Linux is pretty much dead...

AFAIK, Bio-Linux is pretty much dead (http://www.bioinformatics.org/pipermail/bio-linux-list/2016-January/001041.html). If you want to learn bioinformatics, install e.g. Debian Stable, latest Ubuntu...
Forum: Bioinformatics 06-12-2016, 10:41 PM
Replies: 5
Views: 1,359
Posted By rhinoceros
Returns at max 1 hit per sequence though..

Returns at max 1 hit per sequence though..
Forum: Bioinformatics 05-26-2016, 12:24 AM
Replies: 4
Views: 750
Posted By rhinoceros
Saving positional information is a lot of...

Saving positional information is a lot of overhead for k-mer counting algorithms so I'm not so sure it has been implemented in any of them..
Forum: Bioinformatics 05-24-2016, 02:02 AM
Replies: 4
Views: 750
Posted By rhinoceros
You can always map the k-mers back to the genome...

You can always map the k-mers back to the genome with e.g. bowtie2..
Forum: Bioinformatics 03-03-2016, 12:30 AM
Replies: 1
Views: 529
Posted By rhinoceros
grep "pass$" file.fasta >...

grep "pass$" file.fasta > headers_that_end_in_pass.txt

grep "pass$" file.fasta | cut -c 2- > headers_that_end_in_pass_without_the_>.txt
Forum: Bioinformatics 01-04-2016, 10:52 PM
Replies: 15
Views: 3,083
Posted By rhinoceros
In my experience, IDBA-UD assembles metagenomes...

In my experience, IDBA-UD assembles metagenomes way better than Megahit. Can't comment on your QC procedures. For Illumina QC, I've used Trim Galore exclusively. As to odd coverage results, perhaps...
Forum: Bioinformatics 12-07-2015, 05:26 AM
Replies: 4
Views: 1,104
Posted By rhinoceros
Give some metagenome assembler like IDBA-UD a...

Give some metagenome assembler like IDBA-UD a try. It takes into account read coverage. Chances are high that your strains were not present in the isolated DNA in equal abundance. Also set very...
Forum: General 09-09-2015, 10:34 PM
Replies: 9
Views: 1,899
Posted By rhinoceros
Hi. I picked up stuff mostly from the manual and...

Hi. I picked up stuff mostly from the manual and random google searches. Whatever applies to eutils can also be achieved with edirect with little experimentation. For the wgs, you link through the db...
Forum: General 09-08-2015, 11:36 PM
Replies: 9
Views: 1,899
Posted By rhinoceros
It's essentially: esearch -db genome -query...

It's essentially:

esearch -db genome -query PRJNA35077 | elink -target nuccore | efetch -format fasta

However, in real life this fetches too much data because multiple genomes are associated...
Forum: General 09-07-2015, 10:11 PM
Replies: 9
Views: 1,899
Posted By rhinoceros
Perhaps you could post a few examples of project...

Perhaps you could post a few examples of project numbers?
Forum: General 09-06-2015, 11:34 PM
Replies: 9
Views: 1,899
Posted By rhinoceros
If you have genome id's, then simply: efetch...

If you have genome id's, then simply:

efetch -db nuccore -id $ID -format fasta
Forum: Bioinformatics 08-05-2015, 12:38 AM
Replies: 2
Views: 829
Posted By rhinoceros
You could try to set -gapopen and -gapextend to...

You could try to set -gapopen and -gapextend to "0". I'm not so sure it will change the % identity value though..
Forum: Bioinformatics 05-24-2015, 11:31 PM
Replies: 2
Views: 2,290
Posted By rhinoceros
By nr directory do you mean that you have the...

By nr directory do you mean that you have the unzipped files in:

/media/sf_F_DRIVE/nr/*

instead of

/media/sf_F_DRIVE/*

If yes, there's your problem. You should provide the full path,...
Forum: Bioinformatics 05-18-2015, 04:01 AM
Replies: 7
Views: 2,133
Posted By rhinoceros
You could remove the linebreaks in seqs and then...

You could remove the linebreaks in seqs and then continue as Richard advised..


awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' file.fa > out.fa
Forum: Bioinformatics 05-12-2015, 02:21 AM
Replies: 14
Views: 3,192
Posted By rhinoceros
Your optimal max k-mer setting should be about...

Your optimal max k-mer setting should be about your trimmed read length so something like 250, not 600. As to memory, in the context of assembly, 64 GB is very little RAM and the most likely reason...
Forum: Bioinformatics 05-12-2015, 01:50 AM
Replies: 14
Views: 3,192
Posted By rhinoceros
Did you compile idba_ud for a larger max k-mer...

Did you compile idba_ud for a larger max k-mer value (I would have)? Based on your message, we can only guess why it's crashing. I'm assuming you have processed your PE reads into interleaved fasta...
Forum: Bioinformatics 05-07-2015, 04:26 AM
Replies: 132
Views: 35,035
Posted By rhinoceros
Thats great. Do you have any hints how to...

Thats great.

Do you have any hints how to trim ScriptSeq prepped samples? My PE reads clearly had Truseq adaptors, but after trim_galore fastqc tells me that my R1 reads still contain a...
Forum: Bioinformatics 05-07-2015, 12:29 AM
Replies: 132
Views: 35,035
Posted By rhinoceros
There's a small problem with the zip file. ...

There's a small problem with the zip file.


unzip trim_galore_v0.4.0.zip
Archive: trim_galore_v0.4.0.zip
inflating: Trim_Galore_User_Guide.pdf
inflating: trim_galore
...
Forum: Bioinformatics 04-24-2015, 01:34 AM
Replies: 5
Views: 1,713
Posted By rhinoceros
I have to admit that I'm a little bit ignorant on...

I have to admit that I'm a little bit ignorant on the technical details of the sequencing part. Is library size cut off related to fragment size distribution? Also, what is the relation of fragment...
Forum: Bioinformatics 04-24-2015, 12:12 AM
Replies: 5
Views: 1,713
Posted By rhinoceros
Thanks for the reply. About the 3'-end, I'm...

Thanks for the reply. About the 3'-end, I'm indeed most likely overtrimming. In trim_galore:


--stringency <INT> Overlap with adapter sequence required to trim a sequence. Defaults to a very...
Forum: Bioinformatics 04-23-2015, 11:17 PM
Replies: 5
Views: 1,713
Posted By rhinoceros
Question Cleaning paired-end Nextera prepped reads

These reads were sequenced (2x100) with Hiseq 2500 rapid mode. In the first pictures, the reads as they were when I got them:

R1
http://i.imgur.com/Kgeyx9T.png
http://i.imgur.com/IjCBhW9.png...
Forum: Bioinformatics 04-21-2015, 03:28 AM
Replies: 132
Views: 35,035
Posted By rhinoceros
Is this still the case in 2015? I mean, is...

Is this still the case in 2015? I mean, is "CTGTCTCTTATACACATCT" universal to Nextera prepped samples?
Forum: Bioinformatics 02-10-2015, 01:56 AM
Replies: 6
Views: 1,487
Posted By rhinoceros
For a server/workstation, IMO Debian or some...

For a server/workstation, IMO Debian or some derivative. Our cluster runs Rocks, which is based on CentOS..
Forum: Bioinformatics 02-09-2015, 10:22 PM
Replies: 5
Views: 1,937
Posted By rhinoceros
It could be related to the stable bug...

It could be related to the stable bug (http://drive5.com/muscle/stable.html). The stable option was removed from later versions of muscle but hal depends on a version that has it..
Forum: General 02-03-2015, 05:13 AM
Replies: 7
Views: 1,836
Posted By rhinoceros
2. Some assemblers require input in fasta format,...

2. Some assemblers require input in fasta format, e.g. IDBA wants pairs to be consecutive sequences in fasta format and they have bundled a small script for converting from fastq to fasta..

Also,...
Showing results 1 to 25 of 372

 


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