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Search: Posts Made By: rbagnall
Forum: Bioinformatics 11-25-2014, 02:04 AM
Replies: 7
Views: 1,422
Posted By rbagnall
I think that is part of the indexing by USCS for...

I think that is part of the indexing by USCS for faster searching. You can ignore it.
Forum: Bioinformatics 11-24-2014, 04:10 PM
Replies: 7
Views: 1,422
Posted By rbagnall
From UCSC, a table of microRNA binding sites as...

From UCSC, a table of microRNA binding sites as predicted by Target scan:

ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/targetScanS.txt.gz

which looks like this:
...
Forum: Bioinformatics 10-07-2014, 04:31 AM
Replies: 8
Views: 2,704
Posted By rbagnall
java version "1.7.0_02" My vcf files were...

java version "1.7.0_02"

My vcf files were single sample, so no 0/0 calls.

Perhaps show the full command that you write.
Forum: Bioinformatics 10-05-2014, 06:24 PM
Replies: 8
Views: 2,704
Posted By rbagnall
You could restrict variants in the vcf file to...

You could restrict variants in the vcf file to the provided .bed file using Bedtools (intersectBed)
Forum: Bioinformatics 10-03-2014, 10:08 PM
Replies: 8
Views: 2,704
Posted By rbagnall
You need to move to the similarity folder where...

You need to move to the similarity folder where the jar file is located:

1. change directory to the similarity folder

cd path/to/Similarity_05022013

2. Make a new folder for results, called...
Forum: Bioinformatics 10-03-2014, 03:50 PM
Replies: 8
Views: 2,704
Posted By rbagnall
I asked the same question and found the...

I asked the same question and found the Similarity tool on Gentalk's website helpful for this. You can download from here, and it was easy to use:

https://gene-talk.de/qc (and see referenced paper...
Forum: Bioinformatics 06-26-2014, 03:20 AM
Replies: 14
Views: 3,545
Posted By rbagnall
GATK -L interval files do not need a header. They...

GATK -L interval files do not need a header. They should be this format:

chr1:1000-1200
chr1:2004-2507
chr2:457290-457400

etc...
Forum: Bioinformatics 04-16-2014, 10:11 PM
Replies: 2
Views: 1,638
Posted By rbagnall
SeattleSeq Variation annotation tool. Apart from...

SeattleSeq Variation annotation tool. Apart from annotating missense/nonsense/splice etc. it annotates polyphen prediction and KEGG pathway

http://snp.gs.washington.edu/SeattleSeqAnnotation138/
Forum: Bioinformatics 02-05-2014, 06:43 PM
Replies: 3
Views: 1,299
Posted By rbagnall
If you have the chromosome co-ordinates of your...

If you have the chromosome co-ordinates of your SNPs, you could use Bedtools.

Save your list of SNPs in bed format as SNP.bed

chr1 100 101 rs1
chr1 105 106 rs2
chr1 110 111 rs3
chr1 5000 ...
Forum: Bioinformatics 02-04-2014, 01:44 PM
Replies: 10
Views: 3,143
Posted By rbagnall
First you need to register with GATK. At the top...

First you need to register with GATK. At the top of the home page there is a 'Forum' option, and within there is the option to 'Register'.

Once registered and signed in, you can post a new...
Forum: Bioinformatics 01-29-2014, 04:11 PM
Replies: 10
Views: 3,143
Posted By rbagnall
A reported error in GATK ...

A reported error in GATK

http://www.broadinstitute.org/gatk/search?q=Somehow+the+requested+coordinate+is+not+covered+by+the+read.+Too+many+deletions%3F

Update your version from version...
Forum: Bioinformatics 11-18-2013, 03:32 PM
Replies: 1
Views: 1,768
Posted By rbagnall
Determine ethnicity from exome sequence

I have data from 40 exomes and they are from de-identified post-mortem samples.

There are many SNPs that have a higher frequency in Asian populations compared to Europeans, for example. When I...
Forum: Bioinformatics 10-30-2013, 06:37 PM
Replies: 11
Views: 5,932
Posted By rbagnall
Hi DrCheymus, Your Bed file should be tab...

Hi DrCheymus,

Your Bed file should be tab delimited - it was not clear from your post.

Also, try removing the chr from the beginning of each line of the bed file, since if the reference...
Forum: Bioinformatics 10-23-2013, 04:56 PM
Replies: 5
Views: 4,110
Posted By rbagnall
Hi, Since you already have BAM files on your...

Hi,

Since you already have BAM files on your samples, it would take a couple of hours to run GATK universal genotyper with the hard filters, using the best practice guidelines. If the variant you...
Forum: Bioinformatics 10-22-2013, 02:40 PM
Replies: 6
Views: 3,845
Posted By rbagnall
I would recommend SeattleSeq Annotation on-line...

I would recommend SeattleSeq Annotation on-line tool too.

Upload a vcf (can be SNPs and indels) and it will e-mail back a flat text file annotated with gene, mutation type (missense, splice,...
Forum: Bioinformatics 10-21-2013, 03:32 PM
Replies: 5
Views: 4,110
Posted By rbagnall
Hi evakoe, One explanation may be that the...

Hi evakoe,

One explanation may be that the Illumina TruSeq exome (62Mb) includes untranslated regions, both 5' and 3', in the target regions - it has one of the largest target regions of all the...
Forum: Bioinformatics 07-10-2013, 07:40 PM
Replies: 2
Views: 1,498
Posted By rbagnall
Hi desmo, Download the following refseq file...

Hi desmo,

Download the following refseq file (~40Mb)

ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz

unzip and use UNIX grep for the pattern A1CF

grep "A1CF"...
Forum: General 06-16-2013, 02:02 PM
Replies: 9
Views: 2,214
Posted By rbagnall
Gaaaaarrrrrhhhh, STOP!!! You already have...

Gaaaaarrrrrhhhh, STOP!!!

You already have paired end read data. The first file contains the forward reads and the second file contains the reverse reads.
Forum: General 06-16-2013, 03:23 AM
Replies: 9
Views: 2,214
Posted By rbagnall
Hi YOLO69SWAG, I assume you are staring...

Hi YOLO69SWAG,

I assume you are staring with single end reads, not paired end as stated. Trimmomatic may be able to split 100bp single end reads into two 50bp read files.
...
Forum: Bioinformatics 05-09-2013, 06:41 PM
Replies: 2
Views: 1,261
Posted By rbagnall
Hi Inma, I too have seen this. BWA can trim...

Hi Inma,

I too have seen this. BWA can trim reads with low quality, and if there is a difficult-to-sequence region, such as a homopolymer run, then many reads will have low quality at that...
Forum: Bioinformatics 02-21-2013, 02:58 PM
Replies: 8
Views: 3,562
Posted By rbagnall
Hi kjaja, Sorry, there was an extra close...

Hi kjaja,

Sorry, there was an extra close parenthesis ) in the awk command. I have corrected it.
Forum: Bioinformatics 02-20-2013, 06:06 PM
Replies: 8
Views: 3,562
Posted By rbagnall
I also use Bedtools. You need coverageBed with...

I also use Bedtools. You need coverageBed with the -d option to show the coverage per base...

samtools view -b bamfile.bam | coverageBed -abam stdin -b intervals.bed -d > per_base_coverage.txt
...
Forum: Introductions 01-25-2013, 01:57 AM
Replies: 4
Views: 943
Posted By rbagnall
Hi alex95037, I would highly recommend this...

Hi alex95037,

I would highly recommend this free Unix and Perl primer for Biologists from the Korf Lab.

http://korflab.ucdavis.edu/Unix_and_Perl/index.html

I knew no Unix or Perl before...
Forum: Illumina/Solexa 11-21-2012, 05:54 PM
Replies: 1
Views: 15,066
Posted By rbagnall
Resurrecting an old post here, but I need help...

Resurrecting an old post here, but I need help with a related issue. Illumina have a note describing their system for genotype calling from array data
...
Forum: Bioinformatics 11-10-2012, 09:22 PM
Replies: 3
Views: 1,650
Posted By rbagnall
Most likely it has not been added to your perl...

Most likely it has not been added to your perl path (which means that perl cannot find the samtools application). To test this, open terminal and type:

which samtools

and this should display...
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