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Forum: Bioinformatics 02-14-2017, 01:37 PM
Replies: 4
Views: 759
Posted By swbarnes2
Get flanking DNA sequence for your locus, and do...

Get flanking DNA sequence for your locus, and do blastx against a database of proteins. Then parse the blastx results. Let blastx figure out the right frame and orientation.
Forum: Bioinformatics 10-12-2015, 12:41 PM
Replies: 12
Views: 3,702
Posted By swbarnes2
10x might be okay to find clonal mutations, but...

10x might be okay to find clonal mutations, but it's not sufficient for do novo assembly. 50x would be the minimum there.

Your holes in the assembly will be caused by long repetitive things like...
Forum: Bioinformatics 07-01-2015, 12:06 PM
Replies: 3
Views: 1,034
Posted By swbarnes2
I don't think anyone wants to write a blast...

I don't think anyone wants to write a blast parser for you. If you are using blast from the command line, you can tell it to format the output a number of ways, one of those ways might be easier to...
Forum: Bioinformatics 07-01-2015, 11:54 AM
Replies: 3
Views: 802
Posted By swbarnes2
samtools mpileup should also take as a commend...

samtools mpileup should also take as a commend line entry a position, or a bed file of positions, so you don't need to generate a line for every base in the genome.
Forum: Bioinformatics 06-22-2015, 03:16 PM
Replies: 16
Views: 10,647
Posted By swbarnes2
In the future, you really need to include the...

In the future, you really need to include the exact command line you are using.

I'm pretty sure the problem is this: BED format is valid with only three columns of data, but I think coverageBed...
Forum: Bioinformatics 06-18-2015, 11:02 AM
Replies: 19
Views: 6,778
Posted By swbarnes2
Picard tools can also randomly downsample a .bam...

Picard tools can also randomly downsample a .bam file.

And the cheesy way to do it yourself would be to use awk or grep to only grab reads from a particular tile, one not on the edge would be...
Forum: Bioinformatics 06-16-2015, 11:20 AM
Replies: 1
Views: 874
Posted By swbarnes2
RPKM is counts, but corrected for differences in...

RPKM is counts, but corrected for differences in gene length between genes, and differences in overall read numbers between samples. You certainly do need to correct for the fact that not all...
Forum: Bioinformatics 06-16-2015, 11:14 AM
Replies: 19
Views: 6,778
Posted By swbarnes2
I'm still using samtools 0.1.19, can someone just...

I'm still using samtools 0.1.19, can someone just post the portion of vcfutils that is causing the problem? It's a perl script, you can open it in any text editor. I feel like I've seen that error...
Forum: Bioinformatics 02-25-2015, 03:21 PM
Replies: 9
Views: 1,256
Posted By swbarnes2
Did you check to see if bowtie will take a .bam...

Did you check to see if bowtie will take a .bam as input, instead of a fastq?

My version, which might be a little old says it has an option

-r query input files are raw...
Forum: Bioinformatics 02-19-2015, 02:47 PM
Replies: 2
Views: 976
Posted By swbarnes2
Is ucsc.hg19.fasta in that directory? Is it...

Is ucsc.hg19.fasta in that directory? Is it properly indexed?
Forum: Bioinformatics 02-11-2015, 12:04 PM
Replies: 6
Views: 3,823
Posted By swbarnes2
I think Picard's sortSam puts a line in the...

I think Picard's sortSam puts a line in the header indicating that the file is sorted, which samtools does not. But for lots of applications this doesn't matter.
Forum: Bioinformatics 10-01-2014, 03:14 PM
Replies: 1
Views: 3,208
Posted By swbarnes2
The DP4 part spells out how many reads aligned to...

The DP4 part spells out how many reads aligned to reference and alternate allele. So you can parse based on that. You could do that with some finagling in Excel, if you had to.
Forum: Bioinformatics 08-20-2014, 10:44 AM
Replies: 8
Views: 1,741
Posted By swbarnes2
Thank you. I didn't want to do that until I had...

Thank you. I didn't want to do that until I had some confirmation that other people were seeing the problem.
Forum: Bioinformatics 08-20-2014, 10:42 AM
Replies: 5
Views: 2,235
Posted By swbarnes2
Don't mask repeated regions before mapping. If a...

Don't mask repeated regions before mapping. If a read is repetitive, you want it to map to where it belongs. You don't want it forced to map to the wrong place, because you masked away the right...
Forum: Bioinformatics 08-19-2014, 03:15 PM
Replies: 8
Views: 1,741
Posted By swbarnes2
I went into the htslib-1.0 folder of my samtools...

I went into the htslib-1.0 folder of my samtools 1.0 folder, and "make" seems to finish without errors, but samtools 1.0 still does the same thing: idxstats run from the v 1.0 indexing shows only 1...
Forum: Bioinformatics 08-19-2014, 11:05 AM
Replies: 8
Views: 1,741
Posted By swbarnes2
Issue with new samtools 1.0 index and idxstats

When using samtools 1.19, I would index my .bam, and use idxstatst to make a file of read counts per sequence in my reference, and the unmapped reads would be at the bottom of the list.

The line...
Forum: Bioinformatics 08-12-2014, 11:12 AM
Replies: 6
Views: 1,351
Posted By swbarnes2
It would take longer, but swap the second awk in...

It would take longer, but swap the second awk in Richard's command line with

sort -nr

To get the most common reads in order, starting with the most abundant. Tack a

| head -n 100 to get...
Forum: Bioinformatics 08-11-2014, 03:31 PM
Replies: 3
Views: 861
Posted By swbarnes2
There are programs like SNPEff and Annovar, and...

There are programs like SNPEff and Annovar, and ensembl's Variant effect predictor, which will take genomic coordinates, and output differences with respect to genes and amino acids.

If you wanted...
Forum: Bioinformatics 08-06-2014, 03:36 PM
Replies: 8
Views: 1,498
Posted By swbarnes2
Well, don't merge them into 1 file, that's just...

Well, don't merge them into 1 file, that's just throwing away real paired information.

You want all of the read 1 data in one fastq, and all the read 2 data in a second. Just make sure that the...
Forum: Bioinformatics 08-06-2014, 03:30 PM
Replies: 2
Views: 1,421
Posted By swbarnes2
First thing to check...I wonder if one file is...

First thing to check...I wonder if one file is sorted chr1, chr2, chr3...and the other chr1, chr10, chr11...

That discrepancy might explain why the file stops at Chr1.
Forum: Bioinformatics 08-06-2014, 03:28 PM
Replies: 3
Views: 1,140
Posted By swbarnes2
At first glance, it looks like the default...

At first glance, it looks like the default quality filtering differs between the two, samtools 1.19 is more stringent. The ! in the quality string indicates the lower possible quality, the 1.18...
Forum: Bioinformatics 08-05-2014, 03:29 PM
Replies: 8
Views: 1,498
Posted By swbarnes2
The .bam from bgi reports the exact same number...

The .bam from bgi reports the exact same number of read 1 reads as read 2 reads. Yours does not. Are you sure that giving it 4 fastq files at once is the proper way to use bwa mem? I wonder if it...
Forum: Bioinformatics 07-24-2014, 05:06 PM
Replies: 2
Views: 1,689
Posted By swbarnes2
samtools faidx, when given genomic coordinates,...

samtools faidx, when given genomic coordinates, will make a fasta of the desired region. That another way, using software you've already got.
Forum: Bioinformatics 07-23-2014, 12:16 PM
Replies: 2
Views: 702
Posted By swbarnes2
I'd use samtools to make a pileup file, and then...

I'd use samtools to make a pileup file, and then parse the line of the pileup for how many ref and alt letters you see.
Forum: Bioinformatics 07-17-2014, 10:55 AM
Replies: 4
Views: 812
Posted By swbarnes2
Programs like BEDTools can give you the...

Programs like BEDTools can give you the intersection of multiple .vcf files.
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