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Search: Posts Made By: pallevillesen
Forum: Bioinformatics 04-16-2013, 04:44 AM
Replies: 3
Views: 1,082
Posted By pallevillesen
>sort >join cat file1 |sort >file1.sort ...

>sort
>join

cat file1 |sort >file1.sort
cat file2 |sort >file2.sort

[palle@fe1 ~]$ join -v 1 -j 3 file1.sort file2.sort # All lines from file 1 found a match
[palle@fe1 ~]$ join -v 2 -j 3...
Forum: Bioinformatics 02-05-2013, 01:48 AM
Replies: 4
Views: 1,568
Posted By pallevillesen
Use: bedtools intersect -a file1 -b file2...

Use:

bedtools intersect -a file1 -b file2 >overlap_1_2
bedtools intersect -a overlap_1_2 -b file3 >overlap_1_2_3

Works on any SNP caller outputting in vcf / bed format.
Forum: Bioinformatics 01-03-2013, 11:30 PM
Replies: 50
Views: 15,156
Posted By pallevillesen
I'm not sure I complete understand what you...

I'm not sure I complete understand what you actually try to do?

De novo discovery of what? (genes?) You're sequencing an organism with unknown genome sequence? RNA-seq? I can't see what kind of...
Forum: Bioinformatics 01-03-2013, 04:28 AM
Replies: 50
Views: 15,156
Posted By pallevillesen
So have you simply tested the -num_threads...

So have you simply tested the

-num_threads <Integer, >=1>
Number of threads (CPUs) to use in the BLAST search
Default = `1'

option as suggested? And how did it go?

Anyway. for...
Forum: Bioinformatics 12-14-2012, 12:32 AM
Replies: 3
Views: 1,058
Posted By pallevillesen
Some of it is taken care of be the various...

Some of it is taken care of be the various assemblers.

Repeats etc. are identified and distinguished by large insert libraries.

If you have extremely high heterozygosity, it may be a problem...
Forum: Bioinformatics 12-12-2012, 11:06 PM
Replies: 3
Views: 1,957
Posted By pallevillesen
I think there is a problem - but maybe that...

I think there is a problem - but maybe that relates to the genome of your sample(?)

Is it a secret organism - or can you reveal anything? I thought a little more and I have more ugly suggestion:...
Forum: Epigenetics 12-12-2012, 12:42 AM
Replies: 1
Views: 2,073
Posted By pallevillesen
Nope - you just answered your own question ;) ...

Nope - you just answered your own question ;)

You need someone to unzip and map the reads (fastq) to a reference genome (hg19?) and give you the aligned reads (bam) - and format a bedfile for...
Forum: Bioinformatics 12-12-2012, 12:34 AM
Replies: 3
Views: 1,957
Posted By pallevillesen
Your 250 bp library looks a little weird (nearly...

Your 250 bp library looks a little weird (nearly bimodal - or a very "broad" peak).

Other than that you're right - you'll expect up to 4 peaks though:

1. Depth 1-2: sequencing errors
2....
Forum: Bioinformatics 12-12-2012, 12:23 AM
Replies: 1
Views: 731
Posted By pallevillesen
UCSC tables or google "illumina igenomes" ...

UCSC tables or google "illumina igenomes"

http://cufflinks.cbcb.umd.edu/igenomes.html
Forum: Bioinformatics 12-11-2012, 12:09 AM
Replies: 1
Views: 1,051
Posted By pallevillesen
1) ? Reference has nothing - so it's a C...

1) ? Reference has nothing - so it's a C insertion (?) I have never seen this in the documentation or in output... Can't help - sorry.

2) YES! That looks extremely suspicious. Check the raw...
Forum: Bioinformatics 12-10-2012, 11:59 PM
Replies: 10
Views: 11,811
Posted By pallevillesen
Well... Our cluster is brand new with 80 Gbit...

Well... Our cluster is brand new with 80 Gbit network between nodes and the fileserver - that may cause things to run extremely fast here...

Anyway: your problem was solved.
Forum: Bioinformatics 12-06-2012, 11:37 PM
Replies: 10
Views: 11,811
Posted By pallevillesen
I really don't see anything faster than split...

I really don't see anything faster than split (unless you want to parallelize it and let each subroutine extract certain parts of the file) (using e.g. awk).

But for really large files the time...
Forum: Bioinformatics 12-06-2012, 01:03 AM
Replies: 4
Views: 2,704
Posted By pallevillesen
If you're only looking for the intersection of...

If you're only looking for the intersection of all 6 - then you just go

cat 1 | intersect 2 stdin | intersect 3 stdin |intersect 4 stdin |intersect 5 stdin | intersect 6 stdin >out

can't...
Forum: Bioinformatics 12-06-2012, 12:48 AM
Replies: 4
Views: 1,110
Posted By pallevillesen
Ok, if you end up with something like: chr1 ...

Ok, if you end up with something like:

chr1 1002 9005 linRNA1 . + (BED FORMAT)

Then you can

cat combinedfile.bed | sort -k1,1 -k2,2n | uniq >combined.sorted.collapsed.bed

Then it is...
Forum: Bioinformatics 12-04-2012, 10:51 PM
Replies: 3
Views: 1,950
Posted By pallevillesen
mpileup

samtools mpileup -BQ0 -d100000 -f hg19.fa -r chr1:17420-17420 BAMFILE

Will give you the mpileup format for 1 position (then you must parse it). There is a number of parsers around - if you can't...
Forum: Bioinformatics 12-03-2012, 11:32 PM
Replies: 4
Views: 1,110
Posted By pallevillesen
cat file1 >combinedset.txt cat file2...

cat file1 >combinedset.txt
cat file2 >>combinedset.txt
cat file3 >>combinedset.txt

If you need to reformat:
# Column 1,2,3
cat file1 | awk -v "OFS=\t" '{ print $1, $2,$3;} >combinedset.txt
#...
Forum: Bioinformatics 09-18-2012, 04:47 AM
Replies: 18
Views: 2,838
Posted By pallevillesen
I'm also curious - you have a mouse model with...

I'm also curious - you have a mouse model with some viruses inserted into the genome - and you would like to get all the integration sites?

Now using RNA-seq data you would like to recover the...
Forum: General 09-10-2012, 05:31 AM
Replies: 9
Views: 5,501
Posted By pallevillesen
...and load that file again on a different...

...and load that file again on a different machine... (after using save.image())

But saving specific/required objects only will make your code nicer (and memory requirements smaller).
Forum: General 09-10-2012, 04:53 AM
Replies: 9
Views: 5,501
Posted By pallevillesen
I suggest you check ?save ?load for...

I suggest you check

?save
?load

for saving specific R objects/data
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