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Search: Posts Made By: lethalfang
Forum: Bioinformatics 09-27-2018, 11:31 PM
Replies: 5
Views: 846
Posted By lethalfang
Try this: cat original.fastq | awk 'NR%8==1 ||...

Try this:
cat original.fastq | awk 'NR%8==1 || NR%8==2 || NR%8==3 || NR%8==4' > first4s.fastq
cat original.fastq | awk 'NR%8==5 || NR%8==6 || NR%8==7 || NR%8==0' > second4s.fastq
Forum: Bioinformatics 08-26-2015, 04:13 PM
Replies: 0
Views: 1,040
Posted By lethalfang
Question cuffdiff results

Looking at some publicly available RNAseq data. I ran cuffdiff on a pair of tumor-normal RNAseq data downloaded from TCGA, and I'm wondering what those results mean.

In the gene_exp.diff or the...
Forum: Bioinformatics 08-12-2015, 04:51 PM
Replies: 10
Views: 11,267
Posted By lethalfang
I'm no longer in this space, so I don't have any...

I'm no longer in this space, so I don't have any stake in this. It's definitely a very difficult problem:

1) Being able to set range for the replicon size, i.e., distance of the two primers,...
Forum: Bioinformatics 07-22-2015, 11:32 PM
Replies: 2
Views: 1,301
Posted By lethalfang
I forgot what my original problem was. The ...

I forgot what my original problem was.
The .predSV.txt file is pretty small, sometimes only ~ 50 lines for the whole genome.
Have you tried the whole genome and saw an empty file?
Forum: Literature Watch 04-06-2015, 11:15 AM
Replies: 41
Views: 16,999
Posted By lethalfang
Thanks. For the second run where I was having...

Thanks. For the second run where I was having question, there is no error message, and a bunch of .targetcoverage.cnn files are generated.

The status messages are:

Summary: #bins=292,...
Forum: Literature Watch 04-06-2015, 10:44 AM
Replies: 41
Views: 16,999
Posted By lethalfang
When I tried to run more tumor samples using the...

When I tried to run more tumor samples using the reference .cnn file from a past normal run, there is no .cnr output.

This gives me .cnr files:
cnvkit.py batch T1.bam T2.bam T3.bam T4.bam T5.bam...
Forum: Bioinformatics 03-25-2015, 11:46 AM
Replies: 10
Views: 16,220
Posted By lethalfang
I considered "variant allele frequency" as the...

I considered "variant allele frequency" as the frequency of variant alleles in a given sample.
So the tumor's variant allele frequency does not care what's in the normal tissue, and vice versa. ...
Forum: Bioinformatics 01-20-2015, 09:06 AM
Replies: 8
Views: 11,514
Posted By lethalfang
What about samtools | mpileup | bcftools in...

What about samtools | mpileup | bcftools in particular?
I know mpileup has a default base quality of 13 and mapping quality of 0, but that's "raw depth" right?
What does samtools' high-quality...
Forum: Bioinformatics 01-19-2015, 03:51 PM
Replies: 8
Views: 11,514
Posted By lethalfang
Anyone knows exactly what constitutes "high...

Anyone knows exactly what constitutes "high quality" in DP4?
Forum: Bioinformatics 09-10-2014, 10:12 AM
Replies: 10
Views: 16,220
Posted By lethalfang
That's something I used to do a couple of years...

That's something I used to do a couple of years ago.
I just had a script to get those information out of the Strelka output vcf file. I had all those Strelka out directories in a single location,...
Forum: Bioinformatics 08-26-2014, 04:06 PM
Replies: 2
Views: 1,943
Posted By lethalfang
How to find TCGA data in cghub?

We have gotten access approval for some TCGA data, but how do I find them? I have GeneTorrent (gtdownload and cgquery) installed, but it seems mightily difficult to find anything I'm looking for.
...
Forum: Bioinformatics 07-29-2014, 11:51 AM
Replies: 2
Views: 1,301
Posted By lethalfang
Question CREST outputs: what's wrong?

Spent many days to get all the CREST dependencies to run, and anyone knows what this means?


CREST.pl -f tumor.bam.cover.somatic.cover -d tumor.bam -g normal.bam --ref_genome...
Forum: Bioinformatics 07-16-2014, 10:25 AM
Replies: 0
Views: 462
Posted By lethalfang
Understand the mapability wig file values

#bedGraph section chr1:10000-81873
chr1 10000 10014 0.00277778
chr1 10014 10015 0.333333
chr1 10015 10026 0.5
chr1 10026 10031 1
chr1 10031 10036 0.5
chr1 10036 10037 0.333333...
Forum: Bioinformatics 06-13-2014, 03:08 PM
Replies: 0
Views: 1,882
Posted By lethalfang
TruSeq Manifest File: 0 or 1-based coordinate?

I just want to make sure, since there is no standard in these kind of things.

For the Manifest File hosted here:...
Forum: Bioinformatics 06-08-2014, 09:12 PM
Replies: 0
Views: 802
Posted By lethalfang
How to parse the bases string in pileup file

Does anyone know of a simple way to parse the base string of a pileup file into each call?
I want to parse it using the regex of Python, but I find a bit challenging to parse things like, ...
Forum: Bioinformatics 05-25-2014, 01:27 PM
Replies: 0
Views: 1,519
Posted By lethalfang
Trying to make sense of cufflinks output (--GTF vs. --GTF-guide)

Hi guys,

This isn't the first time this question is posted on this board, but I haven't found an answer yet. :D

I tested out Cufflinks on a TCGA data set, using both -GTF and -GTF-guide...
Forum: Bioinformatics 05-22-2014, 11:58 AM
Replies: 1
Views: 867
Posted By lethalfang
Question Control-FREEC, input for ploidy

Control-FREEC has an input for ploidy.

I wonder what is considered a better practice (ploidy=2 or ploidy=4) if I'm looking at a near-tetraploid cancer tissue like this in a tumor-normal pair: ...
Forum: Bioinformatics 05-22-2014, 11:09 AM
Replies: 12
Views: 1,852
Posted By lethalfang
You may have mostly positions that are only...

You may have mostly positions that are only called in one single replicates.

Try this as a test, just to extract only those positions that exist in all 5 replicates, to see if things are working...
Forum: Bioinformatics 05-22-2014, 10:53 AM
Replies: 12
Views: 1,852
Posted By lethalfang
Can you show me a few rows of the output?

Can you show me a few rows of the output?
Forum: Bioinformatics 05-22-2014, 08:29 AM
Replies: 12
Views: 1,852
Posted By lethalfang
There is only one such column? If you combine 5...

There is only one such column? If you combine 5 samples (replicates), there should be 5 such columns.
If not, make sure the header for the sample info are different in each of the 5 vcf files....
Forum: Bioinformatics 05-21-2014, 01:19 PM
Replies: 12
Views: 1,852
Posted By lethalfang
What will this give you? java -Xmx2g...

What will this give you?



java -Xmx2g -jar GenomeAnalysisTK.jar \
-R ref.fasta \
-T CombineVariants \
-minN 2 \
--variant rep1.vcf \
--variant rep2.vcf \
Forum: Bioinformatics 05-21-2014, 01:01 PM
Replies: 12
Views: 1,852
Posted By lethalfang
Does that mean only 1 replicate has that called...

Does that mean only 1 replicate has that called variant?
Forum: Bioinformatics 05-21-2014, 12:56 PM
Replies: 12
Views: 1,852
Posted By lethalfang
http://www.broadinstitute.org/gatk/gatkdocs/org_br...

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_CombineVariants.html

If you want to only show variants in 2+ duplicates, use "--minimumN 2" option.
Forum: Bioinformatics 05-19-2014, 10:47 AM
Replies: 1
Views: 2,610
Posted By lethalfang
multiIntersectBed, or something like this

Hi,

I'm looking for overlapping regions from 3 (or more) bed files. multiIntersectBed from bedtools does that. However, I also want other features and information from those bed files be printed...
Forum: Bioinformatics 05-18-2014, 07:57 PM
Replies: 3
Views: 1,582
Posted By lethalfang
Bed file coordinate sorting

Apparently, I don't quite understand how a bed file should be sorted. I can't quite figure out what's wrong.


bedops --ec --everything myData.bed > /dev/null
May use bedops --help for more help....
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