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Forum: Bioinformatics 08-19-2013, 06:40 AM
Replies: 1
Views: 1,309
Posted By Petrichor
How to compare two hsps with each other?

Hi there! I have small problem.

Within BioPerl I use SearchIO to parse my BLAST-output. Within this, the output is a result, which contain Hits, which contain HSPs.

How can I compare two HSPs...
Forum: Bioinformatics 07-29-2013, 02:09 AM
Replies: 3
Views: 1,485
Posted By Petrichor
How to extract those reads, that are not fully aligned in BLAST+?

Hi there!

Like the title says, How do i get those reads, that are not fully aligned in BLAST?
Someone already tried it?
Forum: Bioinformatics 06-19-2013, 04:23 AM
Replies: 0
Views: 1,199
Posted By Petrichor
How excatly does SOAPdenovo2 calculates the total scaffold length?

Hi there!

I've been working with SOAPdenovo2 quiet a while now.
For some extra researches, I took a closer look on the outputfile with the scaffolds and singeltons.(.scaffseq)

When i was...
Forum: Bioinformatics 05-31-2013, 07:30 AM
Replies: 1
Views: 1,655
Posted By Petrichor
How do i get the gap position from my .sam file?

Hi there!

For research purpose i need all the positions of gaps in my .sam file.
I took a look at them with Tablet, but i need the gaps as an extra file.

Is there an automatic way to do so,...
Forum: Bioinformatics 05-13-2013, 06:35 AM
Replies: 1
Views: 1,458
Posted By Petrichor
SOAPdenovo2 standard deviation input?

Hi there!

Within SOAPdenovo2, where can i insert the standard deviation of my average insert size?

Thank you and Best regards,

Petrichor
Forum: De novo discovery 04-29-2013, 06:38 AM
Replies: 2
Views: 2,084
Posted By Petrichor
Hi there! You need to create a .config file....

Hi there!

You need to create a .config file.
( http://soap.genomics.org.cn/soapdenovo.html Appandix A as an example)
Forum: Bioinformatics 04-29-2013, 02:13 AM
Replies: 4
Views: 3,304
Posted By Petrichor
Thanks for the responds! Changed to bowtie2...

Thanks for the responds!

Changed to bowtie2 and used some short awk-commands.
Got some results, hope they will work.
Forum: Bioinformatics 04-26-2013, 01:39 AM
Replies: 4
Views: 3,304
Posted By Petrichor
Average insert size from paired end data

Hi there!

I am searching for a way to get the average insert size from my data, that was not included.
The dataset i am using is paired-end Illumina data and I ran BLAST.

Has someone a clue or...
Forum: Bioinformatics 04-16-2013, 04:06 AM
Replies: 0
Views: 1,208
Posted By Petrichor
Results from SOAPdenovo no variation

Hi there!

I have been using SOAPdenovo for a while.
With my given dataset i came across a few problems.
No matter how much i change the parameters. i just recived two diffrent results.

The...
Forum: Bioinformatics 04-16-2013, 02:57 AM
Replies: 5
Views: 3,492
Posted By Petrichor
Hi there! I just started with it myself so i...

Hi there!

I just started with it myself so i can help you with the first steps.

First you need to create a config-data on your own (Read the MANUAL for further information).
Then you can start...
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