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Search: Posts Made By: Coryza
Forum: Bioinformatics 06-01-2014, 12:15 PM
Replies: 8
Views: 5,020
Posted By Coryza
I'm interested though why you think the entire...

I'm interested though why you think the entire project should be abandoned. If it works on Windows whats wrong with it? ;)
Forum: Bioinformatics 06-01-2014, 12:04 PM
Replies: 8
Views: 5,020
Posted By Coryza
Point is, I'm only there for one more week, so I...

Point is, I'm only there for one more week, so I don't have any time to do something else. I've succesfully compiled Boost now, and I'm stuck with samtools.

checking for boostlib >= 1.38.0... yes...
Forum: Bioinformatics 06-01-2014, 02:17 AM
Replies: 8
Views: 5,020
Posted By Coryza
Tophat2 on Windows 7.

Hi,

For some (not-logical reasons) we are building our RNA pipeline on Windows. This is mainly due to biological people prefering to work with Windows. So i'm trying to install Tophat2 on windows....
Forum: Bioinformatics 04-17-2014, 02:32 AM
Replies: 2
Views: 2,267
Posted By Coryza
Thanks! I used that and identified all the known...

Thanks! I used that and identified all the known SNPs that were in my sample from the dbSnp database. Do you have any ideas of how many known SNP's I can expect in a SKBR3 cell line? I found...
Forum: Bioinformatics 04-16-2014, 05:21 AM
Replies: 2
Views: 2,267
Posted By Coryza
[Annovar] Annotate SNPs in Samples

Hi All,

I want to annotate the SNPs in my data samples via Annovar. But there are so many databases, and parameters, that I'm a little bit lost. Everyone seems to use a different approach,...
Forum: Bioinformatics 04-04-2014, 12:09 PM
Replies: 4
Views: 3,152
Posted By Coryza
True. So when I coverageBed -a [data filtered...

True. So when I coverageBed -a [data filtered exon regions] -b [exons] that should give the same result when genomeCoverageBed -i [data filtered exion regions] -g [genome] -d.?
Forum: Bioinformatics 04-03-2014, 03:22 AM
Replies: 4
Views: 3,152
Posted By Coryza
Calculate Exome Coverage

*// Edit to make the post more clear (Mapping done via Bowtie2).
My problem is that when counting Exome Coverage via coverageBed gives different results than via genomeCoverageBed. So I'm not sure...
Forum: Bioinformatics 03-14-2014, 03:10 AM
Replies: 6
Views: 3,972
Posted By Coryza
As far as I know this are all the cDNA sequences,...

As far as I know this are all the cDNA sequences, forward and reverse data. I was hoping that I could see whenever a pair-end of sequences matches to the forward hg19 genome, or reverse hg19 genome....
Forum: Bioinformatics 03-14-2014, 02:51 AM
Replies: 6
Views: 3,972
Posted By Coryza
Ok thanks! I'll do that. I do have an other...

Ok thanks! I'll do that. I do have an other question perhaps you can answer me, otherwise I'll make a new threat.

I've got Paired-End Illumina data mapped against the Human Hg19. When viewing the...
Forum: Bioinformatics 03-14-2014, 01:29 AM
Replies: 6
Views: 3,972
Posted By Coryza
[Bowtie2] CIGAR string calculation.

Hi All,

The SAM output gives the 1-based leftmost mapping POSition of the first matching base of the reference. I am wondering if it is possible to calculate the last most mapping POSition of the...
Forum: Bioinformatics 03-12-2014, 04:26 AM
Replies: 1
Views: 2,004
Posted By Coryza
With all correct indentations & formats (it works...

With all correct indentations & formats (it works @ someone else) I get the error
"Differing number of BED fields encountered at line: 3. Exiting..."
Forum: Bioinformatics 03-12-2014, 02:24 AM
Replies: 1
Views: 2,004
Posted By Coryza
Question Bedtools - complementBed not working properly

Hi,

I have some strange issues with bedtools using the command complementBed (bio-Linux). When running the example.

A.bed
chr1 100 200
chr1 400 500
chr1 500 800
my.genome
chr1 1000
Forum: Bioinformatics 02-17-2014, 01:43 AM
Replies: 5
Views: 1,290
Posted By Coryza
Yea after bowtie2 I was planning to use tophat2....

Yea after bowtie2 I was planning to use tophat2. But I still don't understand why its a bad idea to don't map our mRNA data against the mRNA references.
Forum: Bioinformatics 02-17-2014, 01:36 AM
Replies: 5
Views: 1,290
Posted By Coryza
Why is it a bad idea to align against the ref...

Why is it a bad idea to align against the ref mRNA? What should I align against too then?
Forum: Bioinformatics 02-17-2014, 01:19 AM
Replies: 5
Views: 1,290
Posted By Coryza
UTR's in Bowtie2 Global Alignment?

I've got paired-end MiSeq RNA data from Illumina, with as far as I know adapters/primers/barcodes clipped off. When mapping this data with bowtie2 against the human reference mRNA's I don't find even...
Forum: Bioinformatics 02-14-2014, 04:48 AM
Replies: 1
Views: 882
Posted By Coryza
Bowtie2 - Own Indexes

I was wondering... perhaps it's a really stupid question but ok. I've got +- 100 control sequences, is it possible to build an own '6 indexes (bt2)' out of that via the bowtie2-build. So that I'm...
Forum: Bioinformatics 02-13-2014, 07:00 AM
Replies: 16
Views: 5,193
Posted By Coryza
It doesn't count is as 'more than once', but as...

It doesn't count is as 'more than once', but as 'unmapped'.... :(
Forum: Bioinformatics 02-13-2014, 06:54 AM
Replies: 16
Views: 5,193
Posted By Coryza
That one isn't counted. Its just that from the...

That one isn't counted. Its just that from the above 3, 2 have been counted and 1* not...
Forum: Bioinformatics 02-13-2014, 06:48 AM
Replies: 16
Views: 5,193
Posted By Coryza
Hereby the "other data (which should be a pair)"...

Hereby the "other data (which should be a pair)" of the R1 read of the first sequence, which was not mapped.

M01452:20:000000000-A6JAA:1:1113:29093:14236 69 BC095405 2846 0 * = 2846 0 [removed...
Forum: Bioinformatics 02-13-2014, 05:22 AM
Replies: 16
Views: 5,193
Posted By Coryza
The last 2 were original 1 pair indeed, but...

The last 2 were original 1 pair indeed, but aren't matched as a pair, hence are tried to map apart. right?
Forum: Bioinformatics 02-13-2014, 04:50 AM
Replies: 16
Views: 5,193
Posted By Coryza
New question... Bowtie2 says that there are 2...

New question... Bowtie2 says that there are 2 sequences (which were excluded as one of the sequences as pair matching), that align only once. However when I look it up manually, i find 3...
Forum: Bioinformatics 02-13-2014, 12:57 AM
Replies: 16
Views: 5,193
Posted By Coryza
I've succesfully divided the CP's from 227201...

I've succesfully divided the CP's from 227201 sequencing pairs compared to the bouwtie2 output.

... [Sequencing] mRNA Reference Sequences: 2000123
... [Sequencing] cDNA Sequences...
Forum: Bioinformatics 02-13-2014, 12:06 AM
Replies: 16
Views: 5,193
Posted By Coryza
1 (2.86%) aligned concordantly exactly 1 time 9...

1 (2.86%) aligned concordantly exactly 1 time
9 (25.71%) aligned concordantly >1 times

R1a AS:i:53 XS:i:54 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:5C1T1T1C15C3T1C10 YS:i:83 YT:Z:CP
R1b...
Forum: Bioinformatics 02-12-2014, 10:21 AM
Replies: 16
Views: 5,193
Posted By Coryza
Can't figure it out. Anyone else has some ideas?

Can't figure it out. Anyone else has some ideas?
Forum: Bioinformatics 02-12-2014, 06:37 AM
Replies: 16
Views: 5,193
Posted By Coryza
I tried looking at the XS tag. But all 10 pairs...

I tried looking at the XS tag. But all 10 pairs showed XS taggs... I'll look at t he MAPQ now.
Showing results 1 to 25 of 29

 


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