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Search: Posts Made By: antifolate
Forum: Bioinformatics 09-21-2016, 10:08 PM
Replies: 0
Views: 1,149
Posted By antifolate
Need help understanding what "b-allele" refers to

I'm trying to work with Canvas to find Copy Number Variants in human data. I would appreciate if someone clarified what this input is supposed to be:

--b-allele-vcf=VALUE vcf containing SNV...
Forum: Bioinformatics 02-12-2016, 08:57 AM
Replies: 0
Views: 1,065
Posted By antifolate
Need help understanding the method from this paper

I'm trying to somehow follow the method outlined in this (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638133/#B37) paper for calling breakpoints after assembly and mapping to the reference (see...
Forum: Bioinformatics 01-20-2016, 09:13 PM
Replies: 6
Views: 2,229
Posted By antifolate
Thanks GenoMax! This command worked for me:...

Thanks GenoMax! This command worked for me: samtools view -f 0x2 bamfile
Forum: Bioinformatics 01-20-2016, 01:35 PM
Replies: 6
Views: 2,229
Posted By antifolate
You're exactly right; I used samtools view -b...

You're exactly right; I used samtools view -b -F4 to exclude nonmapped reads. Can I tell it to remove both reads if one is removed, or do I have to Perl that up?
Forum: Bioinformatics 01-20-2016, 01:03 PM
Replies: 6
Views: 2,229
Posted By antifolate
Hi GenoMax, bam is binary. I don't speak...

Hi GenoMax,

bam is binary. I don't speak binary. Did you mean the sam file?
Forum: Bioinformatics 01-20-2016, 11:17 AM
Replies: 6
Views: 2,229
Posted By antifolate
samtools fastq (bam2fq) producing non-paired reads

Hello,

I'm trying to produce 2 fastq files from a bam file with samtools fastq -1 reads1.fastq -2 reads2.fastq but the resulting files don't have matching reads. Some reads in reads1 don't have...
Forum: Bioinformatics 01-06-2016, 11:14 PM
Replies: 10
Views: 2,622
Posted By antifolate
@Brian I got you. I wantto filter the mitos out...

@Brian I got you. I wantto filter the mitos out because, well, I just don't care about them; I want to study structural variation along different parts of the chromosomes. Finding possible duplicate...
Forum: Bioinformatics 01-06-2016, 09:19 PM
Replies: 10
Views: 2,622
Posted By antifolate
Do you mean filtering the mito contigs would...

Do you mean filtering the mito contigs would inflate my numbers in the coverage analysis with BBMap? That makes sense. I meant I would filter them later, for my later steps which are mainly comparing...
Forum: Bioinformatics 01-06-2016, 09:01 PM
Replies: 10
Views: 2,622
Posted By antifolate
Very helpful and informative, as always; thank...

Very helpful and informative, as always; thank you @Brian! I just tried kmercountexact.sh and the output is definitely useful. It's also consistent with what I got by plotting the coverage of each...
Forum: Bioinformatics 01-06-2016, 07:05 PM
Replies: 10
Views: 2,622
Posted By antifolate
I just blasted the scaffolds with the highest...

I just blasted the scaffolds with the highest coverage depth and two of them turned out to be mitochondrial. I guess I'll simply filter those two out. Thanks!

I'm not sure I completely understand...
Forum: Bioinformatics 01-06-2016, 04:02 PM
Replies: 10
Views: 2,622
Posted By antifolate
Thanks @GenoMax. I'm more looking into those...

Thanks @GenoMax. I'm more looking into those repeats that the assembly missed. Like instead of assembling two different scaffolds with average coverage, it assembles one scaffold with double the...
Forum: Bioinformatics 01-06-2016, 12:40 PM
Replies: 6
Views: 2,242
Posted By antifolate
For the record, I wrote Perl scripts to convert...

For the record, I wrote Perl scripts to convert the filtered TSV output into pairwise format, using the original pairwise hits. I then used the pairwise output for visualization.

Since I'm more...
Forum: Bioinformatics 01-06-2016, 11:53 AM
Replies: 10
Views: 2,622
Posted By antifolate
Using BBMap to determine possible repeat scaffolds/contigs

Hello,

I used BBmap to find the coverage of a draft genome I have with this command: bbmap.sh in1=reads1.fq in2=reads2.fq ref=scaffolds.fasta covstats=covstats.txtNow I'd like to use the coverage...
Forum: Bioinformatics 12-30-2015, 03:39 PM
Replies: 6
Views: 2,242
Posted By antifolate
Something as simple as a line connecting matches...

Something as simple as a line connecting matches would be enough. Or maybe coloring matches with the same color. Kablammo is an example, but it doesn't take tsv formats as input...
Forum: Bioinformatics 12-30-2015, 01:46 PM
Replies: 6
Views: 2,242
Posted By antifolate
Hello everyone! Please help. Thanks!

Hello everyone!

Please help.

Thanks!
Forum: Bioinformatics 12-29-2015, 07:48 PM
Replies: 6
Views: 2,242
Posted By antifolate
Visualizing BLAST output

What tools would you recommend to visualize blast tsv output? I found several ones but none of them work with tab (or comma) delimited formats.
Forum: Bioinformatics 12-21-2015, 04:50 PM
Replies: 0
Views: 878
Posted By antifolate
Anyone had a positive experience with the assembler PERGA?

I've recently been trying different assemblers on my data. The latest one I tried is PERGA (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252104/). It caught my attention because it uses machine...
Forum: Bioinformatics 12-17-2015, 12:41 PM
Replies: 0
Views: 862
Posted By antifolate
Does MUMmer reorder the query sequences?

Hello,

I'm using NUcmer and mgaps from MUMmer to find indels between a reference and a draft genome. The mgaps output is neat and almost exactly what I want, but not ordered according to where the...
Forum: Bioinformatics 12-15-2015, 07:31 PM
Replies: 0
Views: 1,116
Posted By antifolate
Getting coverage of each contig from velvet output

Is there a way to get the coverage on each contig from velvet? The Log file gives the median coverage only and I can't really understand the meaning of the coverage in the contig headers.
Forum: Bioinformatics 12-14-2015, 01:32 PM
Replies: 11
Views: 1,935
Posted By antifolate
Thanks for the help.

Thanks for the help.
Forum: Bioinformatics 12-14-2015, 01:01 PM
Replies: 11
Views: 1,935
Posted By antifolate
Thanks Brian. I have a question about edit...

Thanks Brian. I have a question about edit distance: if I allow say editdistance=2, would it catch potentially informative bases after the found adapter? For example, if I have the adapter "ADAPTER"...
Forum: Bioinformatics 12-13-2015, 08:04 PM
Replies: 11
Views: 1,935
Posted By antifolate
How do you specify error rate in BBduk adapter trimming?

Hello,

I'm using BBduk to trim adapter sequences from my reads. From the help manual I see the editdistance and hammingdistance options, but they set a fixed number of mismatches, independent of...
Forum: Bioinformatics 11-30-2015, 09:40 AM
Replies: 2
Views: 868
Posted By antifolate
Thanks @GenoMax. This paper is rich in...

Thanks @GenoMax. This paper is rich in information and I've already learned several things. But the authors don't seem to have studied rearrangements (?) which I'm interested in.
Forum: Bioinformatics 11-30-2015, 09:01 AM
Replies: 2
Views: 868
Posted By antifolate
Need suggestions to quantify genomic activity

Hello,

I'm trying to compare different strands of s.pombe, primarily in terms of genomic activity. What I mean by that is insertions, deletions, and rearrangements. I'm still looking for a good...
Forum: Bioinformatics 11-24-2015, 09:17 AM
Replies: 0
Views: 981
Posted By antifolate
Question: Looking for a genome /draft genome aligner with the these features

I have assembled a draft genome of s. pombe that I would like to compare to the reference. My purpose is to study structural variations (rearrangements, insertions/deletions, etc.) between the two...
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