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Search: Posts Made By: tracecakes
Forum: Bioinformatics 10-22-2019, 10:05 PM
Replies: 0
Views: 527
Posted By tracecakes
single cell RNA seq - cell abundance per cluster

Hi all :)

I have a simple question but cannot find an answer (maybe I am using the wrong search terms?)

We have single cell RNA seq data (10X Genomics) and are interested in cell types present...
Forum: Bioinformatics 04-14-2015, 08:11 PM
Replies: 0
Views: 1,370
Posted By tracecakes
samtools mpileup not filtering reads that fail mapping/base quality filters

Hi all,

I was wondering if anyone could help me with this issue. I am trying to create VCF files using samtools mpileup and would like to filter out reads based on mapping/base quality scores. So...
Forum: Genomic Resequencing 01-27-2014, 08:13 PM
Replies: 1
Views: 1,379
Posted By tracecakes
Targeted resequencing/enrichment for low complexity regions

Hi all,

I am looking into methods that would be able to resequence ~0.5 - 1 Mb region which contains repetitive/GC rich regions. I would like to do this to see if there is a large structural...
Forum: Events / Conferences 01-09-2014, 04:56 PM
Replies: 2
Views: 2,700
Posted By tracecakes
Hi there, maybe you can try SweepFinder or SweeD...

Hi there, maybe you can try SweepFinder or SweeD (based on SweepFinder), Nielson et al 2005. I am about to try it out myself :)

tracecakes
Forum: De novo discovery 01-05-2014, 06:09 PM
Replies: 4
Views: 3,670
Posted By tracecakes
Have you tried the alignment with BWA/samtools or...

Have you tried the alignment with BWA/samtools or as you regularly do with your other FASTQs ? I was able to align my contigs.fa file using bwa bwasw (suitable for longer single reads like the...
Forum: De novo discovery 01-05-2014, 03:06 PM
Replies: 4
Views: 3,670
Posted By tracecakes
Hi there Genomics101, it's been a while since...

Hi there Genomics101, it's been a while since I've worked on this but I could possibly help you out :). What exactly is your question and the background to it ?
Forum: Bioinformatics 11-10-2013, 04:00 PM
Replies: 0
Views: 786
Posted By tracecakes
BLAT of sequence to dog/human reference confounding

Hi all :)

Sorry in advanced if this is not the right place to ask this question, but I've ran out of ideas.

I have a piece of sequence which I am interested in that I obtained from next-gen...
Forum: De novo discovery 10-29-2013, 06:24 PM
Replies: 4
Views: 3,670
Posted By tracecakes
BWA alignment using de novo velvet contigs

Hi all,

-beware for a potentially stupid question-

I am using Velvet for the first time in hope to get a better alignment in a chromosome than just using my regular 100 bp paired end Illumina...
Forum: Bioinformatics 10-22-2013, 09:17 PM
Replies: 1
Views: 1,032
Posted By tracecakes
Calling de novo mutations

Hi all,

Is anybody familiar with calling de novo mutations from whole genome sequences of parent-offspring trios (computationally) ? I have read that samtools and VarScan can do this but I would...
Forum: Bioinformatics 08-13-2013, 05:50 PM
Replies: 3
Views: 2,728
Posted By tracecakes
Thanks for your reply lh3. I have indexed my bam...

Thanks for your reply lh3. I have indexed my bam files and its still not working. :(
Forum: Bioinformatics 08-13-2013, 05:43 PM
Replies: 3
Views: 2,728
Posted By tracecakes
samtools mpileup -r not working

Hi all,

I would like to call SNPs from multiple bam files, one chromosome at a time.

I used the following command to get a vcf file for chromosome 1:

samtools mpileup -Q 20 -q 20 -C 50...
Forum: Genomic Resequencing 07-25-2013, 04:08 PM
Replies: 8
Views: 2,333
Posted By tracecakes
Thanks for the advice guys. SNPsaurus, we do want...

Thanks for the advice guys. SNPsaurus, we do want to call SNPs and genotype and we will probably use the MiSeq. I think I will try the pseudo-read contig approach with velvet... I've never done it or...
Forum: Genomic Resequencing 07-23-2013, 08:51 PM
Replies: 8
Views: 2,333
Posted By tracecakes
Hi everyone, I am in a similar situation and...

Hi everyone,

I am in a similar situation and was wondering if anyone could give me some advice too.

We want to align tiger reads to the cat (felCat5) reference genome, however colleagues have...
Forum: Bioinformatics 07-17-2013, 03:11 AM
Replies: 7
Views: 2,075
Posted By tracecakes
Oops sorry, I totally forgot to mention that I am...

Oops sorry, I totally forgot to mention that I am working with genomic not transcriptomic data.
Forum: Bioinformatics 07-11-2013, 11:31 PM
Replies: 7
Views: 2,075
Posted By tracecakes
hiya all :) I am trying to do something...

hiya all :)

I am trying to do something similar (aligning tiger Illumina paired-end reads with the cat reference genome using BWA). Problem is: I am an extreme noobie. :(.

chadn737 your...
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