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Search: Posts Made By: OTU
Forum: Bioinformatics 10-26-2015, 10:16 AM
Replies: 83
Views: 288,326
Posted By OTU
You realize that you are not doing this manually,...

You realize that you are not doing this manually, right? You usually use a program, which creates overlapping/merging reads and gives you the contig.
Forum: Bioinformatics 10-26-2015, 09:30 AM
Replies: 83
Views: 288,326
Posted By OTU
Sorry, you are right. I meant something...

Sorry, you are right. I meant something different.
Your previous post depicts the assembly process correctly.
What I don't understand is what exactly is your question then?
Forum: Bioinformatics 10-22-2015, 03:59 PM
Replies: 83
Views: 288,326
Posted By OTU
R2 reads are not in a form of reverse complement.

R2 reads are not in a form of reverse complement.
Forum: Bioinformatics 10-22-2015, 03:40 PM
Replies: 83
Views: 288,326
Posted By OTU
what example are you looking for?

what example are you looking for?
Forum: Bioinformatics 10-22-2015, 03:34 PM
Replies: 83
Views: 288,326
Posted By OTU
Left and right are not complements of each other....

Left and right are not complements of each other. They match. That's how they overlap. For denovo assembly try using programs like SOAP denovo
http://soap.genomics.org.cn/soapdenovo.html, or SPADES...
Forum: Bioinformatics 10-22-2015, 02:42 PM
Replies: 83
Views: 288,326
Posted By OTU
Assembly algorithm will depend whether you have a...

Assembly algorithm will depend whether you have a reference genome or not. Is it a metagenome sequencing?
Forum: Bioinformatics 10-22-2015, 02:37 PM
Replies: 83
Views: 288,326
Posted By OTU
No. If you have a fragment of DNA:...

No. If you have a fragment of DNA: ATCGTTGAGCAGACT,
your R1: TAGCAA
and R2: GTCTGA
Forum: Bioinformatics 10-22-2015, 02:21 PM
Replies: 83
Views: 288,326
Posted By OTU
Oh, that's just an example of what paired-end...

Oh, that's just an example of what paired-end pairing looks like.
Forum: Bioinformatics 10-22-2015, 02:05 PM
Replies: 83
Views: 288,326
Posted By OTU
Then you should consider that overlap is...

Then you should consider that overlap is something like:
R1-ATTGCTGTG
-----------ACACTGAAAAGT-R2
Forum: Bioinformatics 10-22-2015, 01:58 PM
Replies: 83
Views: 288,326
Posted By OTU
Don't see why "F1.fq: S1: R1=ATCGTTGAG ...

Don't see why
"F1.fq:
S1: R1=ATCGTTGAG
S2: R1=TGAGCAGAC " would overlap. They only match at 3 bp. Assemblers won't combine them.
Forum: Bioinformatics 10-21-2015, 08:15 AM
Replies: 83
Views: 288,326
Posted By OTU
What is your data on? Metagenome, single genome? ...

What is your data on? Metagenome, single genome?
What sequencing platform did you use? What is the processing computer power that you can use?
Forum: Bioinformatics 01-24-2014, 09:01 AM
Replies: 4
Views: 1,158
Posted By OTU
Thank you! However, I wasn't able to find a way...

Thank you!
However, I wasn't able to find a way to get the information on coverage to be in csv format.
I used this:
samtools depth *bamfile* | awk '{sum+=$3} END { print "Average = ",sum/NR}'...
Forum: Bioinformatics 01-23-2014, 01:02 PM
Replies: 4
Views: 1,158
Posted By OTU
sequence coverage format trouble

Hi everyone!

I am using bowtie2 to map my reads on scaffolds and I would like to know, is there a way to get a coverage calculation in samtools? I know that I can use BEDTools, but how can I get...
Forum: Bioinformatics 01-23-2014, 11:34 AM
Replies: 18
Views: 8,585
Posted By OTU
Yeah! It works! Thank you so much! It took...

Yeah! It works!
Thank you so much!
It took really a long time, to compute this!
Forum: Bioinformatics 01-23-2014, 09:30 AM
Replies: 18
Views: 8,585
Posted By OTU
$ ls -l /home/bwawrik/db/refseq_protein*pal ...

$ ls -l /home/bwawrik/db/refseq_protein*pal
-rw-rw-r-- 1 bwawrik bwawrik 275 Dec 15 19:12 /home/bwawrik/db/refseq_protein.pal
Forum: Bioinformatics 01-23-2014, 09:24 AM
Replies: 18
Views: 8,585
Posted By OTU
I know the problem , why there is not .00 file -...

I know the problem , why there is not .00 file - I accidently deleted it.
I am downloading it now.
And for the checking of '*.pal', we have problems:
$ ls -l /home/bwawrik/db/refseq_protein* |...
Forum: Bioinformatics 01-23-2014, 09:04 AM
Replies: 18
Views: 8,585
Posted By OTU
Ok, so far: $ ls -l...

Ok, so far:
$ ls -l /home/bwawrik/db/refseq_protein* | head --lines=2
-rw-rw-r-- 1 bwawrik bwawrik 534122462 Dec 15 18:37 /home/bwawrik/db/refseq_protein.01.phr
-rw-rw-r-- 1 bwawrik bwawrik ...
Forum: Bioinformatics 01-23-2014, 08:27 AM
Replies: 18
Views: 8,585
Posted By OTU
No problem. So, from previous post, here is the...

No problem.
So, from previous post, here is the full paths included:
$ blastp -query /home/bwawrik/software/multi-metagenome/R.data.generation/IIa.orfs.hmm.faa.db -db...
Forum: Bioinformatics 01-23-2014, 08:02 AM
Replies: 18
Views: 8,585
Posted By OTU
This is what I have done - there were everywhere...

This is what I have done - there were everywhere specified full paths (I just eliminated them from the question). And yes, there are 81 files in the folder db in home directory...
Forum: Bioinformatics 01-23-2014, 07:52 AM
Replies: 18
Views: 8,585
Posted By OTU
Hi everyone! My problem is somehow realted to...

Hi everyone!
My problem is somehow realted to this described issue. I am using a refseq)protein database, downloaded from ncbi ftp, which consists of in total 9 folders with files .pni .pnd .pog and...
Forum: Bioinformatics 09-22-2013, 12:32 PM
Replies: 252
Views: 105,128
Posted By OTU
Xu, Have you specified the output directory...

Xu,

Have you specified the output directory in your command line?
If yes - delete it.
Forum: Bioinformatics 09-12-2013, 02:05 PM
Replies: 15
Views: 17,091
Posted By OTU
It candidate division TM7. It is in Silva,...

It candidate division TM7. It is in Silva, because probes for FISH were designed through ARB...
Forum: Bioinformatics 09-12-2013, 01:56 PM
Replies: 15
Views: 17,091
Posted By OTU
Sorry for confusion! So, sequences are from...

Sorry for confusion!

So, sequences are from sorted cells from water sample, and should be enriched in one candidate division sequences. Cells were lysed and amplified via multiple displacement...
Forum: Bioinformatics 09-12-2013, 01:41 PM
Replies: 15
Views: 17,091
Posted By OTU
The reads are from metagenome, and the reference...

The reads are from metagenome, and the reference is an indexed bowtie library of Silva SSU rRNA genes from all living organisms.
So... I t should give some hits!
Forum: Bioinformatics 09-12-2013, 01:15 PM
Replies: 15
Views: 17,091
Posted By OTU
Hi All! I am facing some kind of the same...

Hi All!

I am facing some kind of the same problem, but all posted possible solutions are not working...
I tried --ff, --fr, --rf - and no result. 0% of alignment. I even tried -U option - no...
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