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Search: Posts Made By: azneto
Forum: Bioinformatics 02-04-2019, 12:35 AM
Replies: 29
Views: 11,645
Posted By azneto
Try this '^@(\S+)\s[1|2]\S+$'

Try this '^@(\S+)\s[1|2]\S+$'
Forum: Bioinformatics 11-30-2016, 09:12 AM
Replies: 3
Views: 1,557
Posted By azneto
You should try 'bcftools merge' ...

You should try 'bcftools merge'

https://samtools.github.io/bcftools/bcftools-man.html#merge

By default it will merge you're samples like this:
1 200 A C,T,-,TT

But you can tweak the -m...
Forum: Bioinformatics 09-01-2016, 10:02 AM
Replies: 8
Views: 1,797
Posted By azneto
I tested your version of the command and it...

I tested your version of the command and it worked fine. It could be something related to permissions.
Forum: Bioinformatics 09-01-2016, 09:39 AM
Replies: 8
Views: 1,797
Posted By azneto
for i in `ls *.fastq.gz`; do gunzip -c $i >...

for i in `ls *.fastq.gz`; do gunzip -c $i > $i.fastq; done
Forum: Bioinformatics 09-01-2016, 08:59 AM
Replies: 8
Views: 1,797
Posted By azneto
have you tried 'gunzip *.fastq.gz' ?

have you tried 'gunzip *.fastq.gz' ?
Forum: Bioinformatics 08-23-2016, 06:51 AM
Replies: 2
Views: 1,369
Posted By azneto
IDBA contains a script called split_scaffold ...

IDBA contains a script called split_scaffold

https://github.com/loneknightpy/idba

Here's what it does:

IN =>

>test...
Forum: Bioinformatics 04-11-2016, 11:45 AM
Replies: 1
Views: 1,215
Posted By azneto
http://journals.plos.org/plosone/article?id=10.137...

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126911
Forum: Bioinformatics 01-07-2016, 08:28 AM
Replies: 6
Views: 1,905
Posted By azneto
I've noticed that and changed my reply. Check it...

I've noticed that and changed my reply. Check it out:

for placeholder1 in `ls *_R1_*.fastq`; do
Forum: Bioinformatics 01-07-2016, 07:46 AM
Replies: 6
Views: 1,905
Posted By azneto
Rather than: placeholder1='name1' ...

Rather than:

placeholder1='name1'
placeholder2='name2'
placeholder3='beginning_of_the_couple_name'

for placeholder1 in *; do

try:
Forum: Bioinformatics 01-07-2016, 07:03 AM
Replies: 6
Views: 1,905
Posted By azneto
You don't need to get both names. Just take the...

You don't need to get both names. Just take the first one use regex to change the _R1_ part or get rid of everything from _R1_

Try this:

placeholder1='name1'
placeholder2=`echo $placeholder1 |...
Forum: Bioinformatics 08-27-2015, 06:11 AM
Replies: 3
Views: 1,076
Posted By azneto
I like to use flash2 to do it...

I like to use flash2 to do it (https://github.com/dstreett/FLASH2).
These software assume both files contain the exact same number of reads.
You should manage to get rid of unpaired reads. ...
Forum: Bioinformatics 03-19-2014, 06:16 AM
Replies: 29
Views: 11,645
Posted By azneto
Hi shatz, The default regex should work. You...

Hi shatz,
The default regex should work.
You can test it by running:

grep -P '@(\S+)\s[1|2]\S+$' yourSequenceFile.fastq

The script does not handle zipped files.
-Best
Forum: Bioinformatics 03-19-2014, 06:13 AM
Replies: 29
Views: 11,645
Posted By azneto
Hi bwubb, The regex is correct. You can...

Hi bwubb,
The regex is correct.
You can test it by running:

grep -P '^@(\S+)\s[1|2]\S+$' yourSequenceFile.fastq

The script does not handle zipped files.
-Best
Forum: Bioinformatics 12-17-2012, 03:16 PM
Replies: 29
Views: 11,645
Posted By azneto
That's really good news bmtb! Cheers Adhemar

That's really good news bmtb!
Cheers
Adhemar
Forum: Bioinformatics 12-17-2012, 03:04 PM
Replies: 29
Views: 11,645
Posted By azneto
Hi bmtb, Sorry it took me so long to reply. ...

Hi bmtb,
Sorry it took me so long to reply.
The version of the script you have uses 40x the size of the f1 file.
I've just attached a version that uses about 6x.
So, if you use the 35GB file as...
Forum: Bioinformatics 08-21-2012, 11:34 AM
Replies: 5
Views: 1,268
Posted By azneto
Bowtie allows you to specify both minimum and...

Bowtie allows you to specify both minimum and maximum insert size. Assemblers usually have the parameters min_ins, avg_ins, and max_ins.
Forum: Bioinformatics 06-01-2012, 06:01 AM
Replies: 3
Views: 1,629
Posted By azneto
The questions from ECO are really important in...

The questions from ECO are really important in order to answer that.
In anyways, I'm having really good results using Bedtools (http://code.google.com/p/bedtools/).
There's this 'coverageBed' tool...
Forum: Bioinformatics 04-15-2012, 05:50 AM
Replies: 4
Views: 2,145
Posted By azneto
http://seqanswers.com/forums/showthread.php?t=1001...

http://seqanswers.com/forums/showthread.php?t=10018
Forum: Bioinformatics 04-14-2012, 11:15 PM
Replies: 4
Views: 2,145
Posted By azneto
http://www.bioperl.org/wiki/HOWTO:SearchIO

http://www.bioperl.org/wiki/HOWTO:SearchIO
Forum: Bioinformatics 02-28-2012, 11:09 AM
Replies: 29
Views: 11,645
Posted By azneto
Hi, It most probably is a memory issue. The...

Hi,
It most probably is a memory issue.
The script loads only the first file into the memory and starts to match with the entries in the second file. You'll have to monitor the memory usage...
Forum: Bioinformatics 02-28-2012, 02:12 AM
Replies: 29
Views: 11,645
Posted By azneto
Hi dejavu2010. ...

Hi dejavu2010.

@HWI-ST829:138:D071VACXX:1:1101:1131:2048 1:N:0:ATCACG.

you can use: '^@(\S+)\s[1|2]\S+$'

Assuming that 1 and 2 will appear right after the space char.
'@' 'ID' 'space'...
Forum: Bioinformatics 02-27-2012, 05:04 AM
Replies: 29
Views: 11,645
Posted By azneto
I wrote a script exactly to tackle that issue....

I wrote a script exactly to tackle that issue. You'll find a copy attached.
The script will output either an interleaved mate pair fastq or two fastq files. The unpaired reads will also be saved in...
Forum: Bioinformatics 01-22-2011, 06:02 AM
Replies: 6
Views: 6,778
Posted By azneto
You definitely should take a look at the remap...

You definitely should take a look at the remap tool from the EMBOSS package.
http://emboss.bioinformatics.nl/cgi-bin/emboss/remap
Cheers,
Adhemar
Forum: Bioinformatics 11-29-2010, 05:48 AM
Replies: 5
Views: 2,221
Posted By azneto
I stumble into this problem and it seems that...

I stumble into this problem and it seems that there's not enough memory for merging the mapping results.

I solved this by altering the following file:

...
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