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Forum: Bioinformatics 01-09-2019, 06:09 AM
Replies: 1
Views: 1,678
Posted By ddaneels
add UMI sequences to fastq read name

Dear all,

I have paired-end fastq data generated with Illumina bcl2fastqv2.19 & sequenced on a Novaseq.The i5index is 7bp long, the i7 8bp long

R1.fastq.gz contains R1 101bp reads:
...
Forum: Bioinformatics 03-29-2013, 06:07 AM
Replies: 8
Views: 11,057
Posted By ddaneels
Can I also find them if I haven't made a design...

Can I also find them if I haven't made a design myself?

I have some exome data from collagues enriched with SureSelect v4, sequenced by BGI. Can I just download the designfiles somewhere from the...
Forum: Illumina/Solexa 03-29-2013, 05:56 AM
Replies: 0
Views: 1,813
Posted By ddaneels
FASTQC Exome 100bp reads Illumina data Nimblegen enrichment

Hi everyone,

I have some exome data generated on an Illumina HiSeq2000 by Otogenetics. The exome capturing was done with Nimblegen v2.

I've generated some FASTQC data and I notice something...
Forum: Bioinformatics 09-27-2012, 12:50 AM
Replies: 8
Views: 6,519
Posted By ddaneels
Your picard value was around 0.13. Is this 0.13%...

Your picard value was around 0.13. Is this 0.13% or do you still need to multiply it with 100. So that it's actually 13 % ?
Forum: Bioinformatics 09-20-2012, 04:26 AM
Replies: 138
Views: 69,340
Posted By ddaneels
I get the following error when using GATK to...

I get the following error when using GATK to perform local realignment around indels.

Anyone an idea what went wrong?


E:\EXOME DATA ANALYSIS\1 Unzipped fastq>java -jar GenomeAnalysisTK.jar...
Forum: Bioinformatics 08-16-2012, 01:40 AM
Replies: 20
Views: 26,524
Posted By ddaneels
my header.sam file looks OK. "chr" has been...

my header.sam file looks OK. "chr" has been added.

But when I run the samtools reheader command, nothing changes in the original .bam file...

Code:
samtools reheader header.sam sample1.bam |...
Forum: Bioinformatics 08-14-2012, 06:44 AM
Replies: 20
Views: 26,524
Posted By ddaneels
Thanks for the info. Everything will work...

Thanks for the info.

Everything will work fine then. I was confused with the "1" in the 7th column of the read-part in the .bam file.

Example:

HWI-ST571_103:4:1302:9610:62449 99 1 604269...
Forum: Bioinformatics 08-14-2012, 05:38 AM
Replies: 20
Views: 26,524
Posted By ddaneels
That would be a way to change the header, but if...

That would be a way to change the header, but if I'm not mistaking the chromosome numbers are also in the actual read-part of the file. So how to change them there?
Forum: Bioinformatics 08-14-2012, 05:15 AM
Replies: 20
Views: 26,524
Posted By ddaneels
This is of course one option ... I'm remapping my...

This is of course one option ... I'm remapping my data for the moment, but since I have 5 .bam files from exome data, it takes quite some time. So I was looking for a faster option :)
Forum: Bioinformatics 08-14-2012, 05:02 AM
Replies: 20
Views: 26,524
Posted By ddaneels
changing chromosome notation in .BAM file

Hi everyone,

I have .bam files in which the chromosomes are notated as '1', '2', '3', ... 'X', 'Y'.
However, for further analyses I need a .bam file in which the chromosomes are notated as...
Forum: Ion Torrent 07-26-2012, 03:51 AM
Replies: 1
Views: 3,227
Posted By ddaneels
CLC BIO for detecting indels in ION Torrent PGM data

Hello everyone,

I was wondering if someone has some experience with using the CLC BIO genomics workbench to call indels in ion torrent PGM data? Did you encounter a lot of false positives in...
Forum: Bioinformatics 05-22-2012, 05:44 AM
Replies: 0
Views: 1,969
Posted By ddaneels
VCF file format QUAL column

Hello,

I'm generating a VCF file which consists of genotype data from 5 individuals. For each variant from each individual I have a Phred Quality Score. But I want to make a VCF file in which I...
Forum: Bioinformatics 04-27-2012, 06:23 AM
Replies: 1
Views: 2,889
Posted By ddaneels
SNP detection CLC Bio

Hi everyone,

I found in the literature that when you do SNP detection in human exome data, you expect approximately 20,000 SNPs

We did exome sequencing with SeqCap Nimblegen v2 30x coverage on...
Forum: Bioinformatics 04-20-2012, 05:25 AM
Replies: 3
Views: 6,055
Posted By ddaneels
dbSNP download

Hi everyone,

I would like to import the dbSNP database into CLC Bio to use it for filterning. Where can I download this? And which format is the best?

I'm analyzing human exome data.
Forum: Bioinformatics 04-13-2012, 12:17 AM
Replies: 138
Views: 69,340
Posted By ddaneels
Trim barcodes

Would it also be a good idea to trim of the Illumina barcode sequences? And to keep only the barcoded reads?
Forum: Bioinformatics 04-12-2012, 10:50 PM
Replies: 138
Views: 69,340
Posted By ddaneels
Thanks for the fast reply! I do have another...

Thanks for the fast reply!

I do have another question: I downloaded the newest UCSC release of the human genome. 7When I unpack this .tar.gz file there are a lot of different files called f.e....
Forum: Bioinformatics 04-12-2012, 09:38 PM
Replies: 138
Views: 69,340
Posted By ddaneels
Hello, Really helpful manual! Nice work! ...

Hello,

Really helpful manual! Nice work!

I saw that you are working with Illumina data. I was wondering if you clipped of the 3' adaptor sequence? If so, with which tool?
Forum: Bioinformatics 04-11-2012, 06:51 AM
Replies: 3
Views: 2,379
Posted By ddaneels
Apologies, instead of 'grep' I meant 'paste'....

Apologies, instead of 'grep' I meant 'paste'. Like you said I tried paste file1.fastq file2.fastq

But I'm not sure that this command does the same as the 'fastq joiner' tool in Galaxy
Forum: Bioinformatics 04-11-2012, 05:10 AM
Replies: 3
Views: 2,379
Posted By ddaneels
Linux Command for joining left & right hand reads

I know that there's a tool in Galaxy called 'Fastq Joiner' in which 2 fastq files (one with left & one with right hand reads) are joined together.
Is there a simple Linux command to do the same...
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