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Search: Posts Made By: Kath
Forum: Bioinformatics 01-07-2016, 01:47 AM
Replies: 1
Views: 4,199
Posted By Kath
ATAC-seq quality control

Hello,

I am analysing ATAC-seq data for the first time and am wondering what typical values are for:

Total number of reads
Duplication rate
Percentage of reads uniquely mapping
Percentage of...
Forum: Bioinformatics 10-21-2013, 06:02 AM
Replies: 6
Views: 2,207
Posted By Kath
I've just got exactly the same with my data. ...

I've just got exactly the same with my data. What kit did you use for capture?

Cheers

Kath
Forum: Bioinformatics 10-01-2013, 07:02 AM
Replies: 2
Views: 1,987
Posted By Kath
Thanks - that does look promising.

Thanks - that does look promising.
Forum: Bioinformatics 09-19-2013, 01:29 AM
Replies: 2
Views: 1,987
Posted By Kath
Publicly available exome data

Hi,

I'm after some publicly available exome data from a trio in which there is a known de novo mutation. I'd like to run it through my pipeline just make sure I can rediscover the de novo...
Forum: Bioinformatics 09-19-2013, 01:25 AM
Replies: 4
Views: 3,890
Posted By Kath
Thanks for your reply. I have Lifescope mapped...

Thanks for your reply. I have Lifescope mapped BAM files but I'm trying to dedup using Picard and am getting some very high duplication rates. I've been told that Picard seems to overestimate...
Forum: Bioinformatics 09-16-2013, 03:12 AM
Replies: 4
Views: 3,890
Posted By Kath
SOLiD paired end data and BWA - cleaning/mapping

Hello everyone,

I notice there has been the odd post about this general topic before but I am still confused!

I have SOLiD single and paired end data which I would like to take through the...
Forum: Bioinformatics 07-18-2013, 04:14 AM
Replies: 1
Views: 1,149
Posted By Kath
Pedigree checking from exome data

Hi,

Can anyone recommend a tool for checking that samples within the same family are not mislabelled using their exome sequencing data. I'm sure there must be a tool which takes in vcfs and ped...
Forum: Bioinformatics 07-15-2013, 05:44 AM
Replies: 1
Views: 1,258
Posted By Kath
Exome sequencing quality filtering

Hi,

I am using exome sequencing data to call variants in patient samples and would like to know what quality control is generally applied before mapping. At the moment I am using...
Forum: Bioinformatics 05-15-2013, 01:00 AM
Replies: 2
Views: 4,684
Posted By Kath
Agilent SureSelect bed files

Hello,

Can anyone tell me what the difference is between these bed files supplied by Agilent for their SureSelect Human All Exon V2 kit:

_Regions.bed
_Padded.bde
_Covered.bed
_AllTargets.bed...
Forum: Bioinformatics 04-24-2013, 01:44 AM
Replies: 3
Views: 3,622
Posted By Kath
FamSeq vs Polymutt vs DeNovoGear

Hi,

I would like to call variants jointly in a trio, taking pedigree info into account. I have heard of three tools for doing this - FamSeq (http://odin.mdacc.tmc.edu/~wwang7/FamSeqIndex.html),...
Forum: Bioinformatics 04-23-2013, 12:14 AM
Replies: 4
Views: 2,864
Posted By Kath
So, UnifiedGenotyper does not use pedigree...

So, UnifiedGenotyper does not use pedigree information. I guess I'll need to use a third-party tool.
Forum: Bioinformatics 04-22-2013, 07:12 AM
Replies: 4
Views: 2,864
Posted By Kath
Thanks Zaag. I have given the GATK website a...

Thanks Zaag. I have given the GATK website a read and also watched all the videos from their workshop on best practices. I realise HaplotypeCaller is supposed to be better than UnifiedGenotyper so...
Forum: Bioinformatics 04-22-2013, 06:21 AM
Replies: 4
Views: 2,864
Posted By Kath
Joint variant calling in trios

Hello,

I have exome sequencing data for a few sets of trios in which the offspring have phenotypically related but probably genetically distinct diseases. The parents are unaffected so I am...
Forum: Bioinformatics 01-13-2011, 01:45 AM
Replies: 1
Views: 3,222
Posted By Kath
UCSC refSeq to rod?

Hi,

I have downloaded the refSeq genes table from the UCSC website and wish to use it with the GATK IndelGenotyper tool. To do this apparently GATK requires reference-ordered data (rod). Does...
Forum: Bioinformatics 12-08-2010, 01:33 AM
Replies: 3
Views: 4,082
Posted By Kath
Thanks for your response. I tried using "R="...

Thanks for your response. I tried using "R=" etc. but now it is saying "invalid argument value" for every argument.

Kath
Forum: Bioinformatics 12-07-2010, 05:56 AM
Replies: 3
Views: 4,082
Posted By Kath
GATK - doesn't see files

Hi,

I'm probably being really stupid but can anyone tell me why GATK is failing to load my reference dictionary. I have a folder containing the fasta files including the .fai, .dict etc. The...
Forum: Bioinformatics 12-01-2010, 02:59 AM
Replies: 4
Views: 5,587
Posted By Kath
Thanks, I hadn't noticed that thread. Kath

Thanks, I hadn't noticed that thread.
Kath
Forum: Bioinformatics 11-30-2010, 08:53 AM
Replies: 4
Views: 5,587
Posted By Kath
Thanks for your response. I had seen the website...

Thanks for your response. I had seen the website but found it assumed more informatics knowledge than I possess. For example, it tells you how to merge two rod files but not how to get the rod for...
Forum: Bioinformatics 11-29-2010, 08:58 AM
Replies: 4
Views: 5,587
Posted By Kath
GATK - dbSNP .rod files

Hi,

I am using GATK to adjust my per base quality scores in a .bam file. Does anyone know how to download a dbSNP v132 .rod file in order to exclude already known variants so they are not...
Forum: Bioinformatics 11-24-2010, 09:06 AM
Replies: 2
Views: 2,460
Posted By Kath
Ah ha, how right you are! Thanks.

Ah ha, how right you are! Thanks.
Forum: Bioinformatics 11-24-2010, 08:43 AM
Replies: 2
Views: 2,460
Posted By Kath
Samtools - index

Hello,

I'm trying to use the SamTools index command. I have installed the latest version (0.1.9) but there doesn't seem to be an "index" in the SamTools folder. Instead there are "bam_index.c"...
Forum: Bioinformatics 11-24-2010, 08:40 AM
Replies: 6
Views: 6,910
Posted By Kath
Ok, setting VALIDATION_STRINGENCY=LENIENT allows...

Ok, setting VALIDATION_STRINGENCY=LENIENT allows the .bam file to be produced. Thanks very much for your help!
Forum: Bioinformatics 11-24-2010, 04:42 AM
Replies: 6
Views: 6,910
Posted By Kath
Thanks for the suggestions. I used BWA to align...

Thanks for the suggestions. I used BWA to align the reads. I didn't realise you could use SAMtools to convert from SAM to BAM.
Forum: Bioinformatics 11-24-2010, 01:36 AM
Replies: 6
Views: 6,910
Posted By Kath
Sam to Bam using Picard - help!

Hi,

I am trying to convert from sam to bam using Picard but am getting an error message (see below). Can anyone interpret this for me?

Thanks!

Kath

[skgtkaf@login01 13655]$ java -jar...
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