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Forum: Bioinformatics 07-01-2016, 11:21 AM
Replies: 0
Views: 1,123
Posted By bsmith030465
sort reference fasta file

Hi,

I need to sort my reference fasta file so that it can be used for analyzing vcfs that were created in galaxy using a sorted reference file. How can I sort my reference file...
Forum: Bioinformatics 06-20-2016, 11:25 AM
Replies: 1
Views: 3,849
Posted By bsmith030465
PLINK: merge bed/bim/fam files error

Hi,

I was trying to merge several files (each chr has separate file) into one big file. I gave the following command:

plink --noweb --bfile T2.chr1 --merge-list mylist.txt --make-bed --out T2
...
Forum: General 04-21-2015, 12:01 PM
Replies: 0
Views: 2,314
Posted By bsmith030465
PLINK: bed to vcf conversion

Hi,

This is really dumb! I looked at the FAQ/online etc., but couldn't find this....

I want to convert my files (xx.bed, xx.bim, xx.fam) to vcf format. I am following the code given at:...
Forum: Bioinformatics 02-26-2015, 09:08 AM
Replies: 6
Views: 3,011
Posted By bsmith030465
Further: 1. I tried using the picard...

Further:

1. I tried using the picard FixMateInformation function, but that didn't seem to help.
2. Tried 'samtools fixmate '*.bam' before merging the files and that seems to help.

Instead of...
Forum: Bioinformatics 02-26-2015, 07:47 AM
Replies: 6
Views: 3,011
Posted By bsmith030465
Thanks for the replies. I have tried the...

Thanks for the replies. I have tried the following steps (see below), but when I try to validate the bam files with picard, I get errors. Am I doing things correctly?

Let me know if you want more...
Forum: Bioinformatics 02-23-2015, 12:41 PM
Replies: 6
Views: 3,011
Posted By bsmith030465
Newbie bwa question (HiSeq data)Hi, Sorry for the newbie question! I am trying to c

Hi,

Sorry for the newbie question!

I am trying to convert output from HiSeq whole genome sequence to bam format that will be used by GATK. For any one sample, I have multiple files, e.g.

...
Forum: Bioinformatics 02-23-2015, 10:23 AM
Replies: 1
Views: 1,719
Posted By bsmith030465
ok, nevermind. My mistake!

ok, nevermind. My mistake!
Forum: Bioinformatics 02-23-2015, 09:47 AM
Replies: 1
Views: 1,719
Posted By bsmith030465
BWA index error

Hi,

I was trying to index the hg19 genome, but get an error:

$ bwa index -a bwtsw /UCSC/human/hg19.fa
[bwa_index] Pack FASTA... [bns_fasta2bntseq] fail to open file '/UCSC/human/hg19.fa.pac' :...
Forum: Bioinformatics 11-10-2014, 08:33 AM
Replies: 5
Views: 2,044
Posted By bsmith030465
Hi max, I am running in an interactive mode...

Hi max,

I am running in an interactive mode - I am executing the commands on one of the nodes. All executable are in /Usr/local/bin, and they (tophat2 & bowtie2) appear to be accessible...
Forum: Bioinformatics 11-10-2014, 05:46 AM
Replies: 5
Views: 2,044
Posted By bsmith030465
tophat2 : Bowtie2 not found...

Hi,

I am new to NGS analysis. I was trying to follow a protocol for an analysis that calls on tophat2 on a cluster. After looking at some previous posts on this forum, I am trying to specify the...
Forum: Introductions 11-10-2014, 05:39 AM
Replies: 0
Views: 715
Posted By bsmith030465
Hello

Just starting out with sequence analysis!
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