User: thecuriousbiologist

Reputation:
430
Status:
Trusted
Location:
United States
Last seen:
4 years, 4 months ago
Joined:
6 years, 9 months ago
Email:
t******************@gmail.com

about me

Posts by thecuriousbiologist

<prev • 23 results • page 1 of 3 • next >
10
votes
2
answers
5.1k
views
2
answers
Validated CNV dataset for NA12878
... Hi,  I was wondering if anybody could point me to public datasets having validated CNV calls from NGS for the Corriell sample NA12878.  I found this old thread  https://www.biostars.org/p/12125/  which says that there is not a standard CNV set available, however the thread is 3.5 years old and I ...
ngs cnv written 4.5 years ago by thecuriousbiologist430 • updated 4.2 years ago by Zev.Kronenberg11k
0
votes
3
answers
5.8k
views
3
answers
Comment: C: Which Pipeline To Analyze Dnase-Seq For Significant Regulatory-Region Finding?
... Hi jasper1918,  As far as I know those are not p-values but are just assigned "-1" in the pvalue column of the NPF format, since the program does not do significance tests. Could you shed more light on how you obtained the p-values with FSeq ?   I tried setting output format as NPF, but I always g ...
written 4.7 years ago by thecuriousbiologist430
9
votes
3
answers
10k
views
10 follow
3
answers
How to extract reads in a specific region from a BAM file and also their mates mapped elsewhere ?
... I have paired-end data as a BAM file and I am trying to extract reads from a specific region. This sounds pretty straightforward, however, the catch is that some of the reads may have their mates mapped in a completely different location, maybe due to large structural variation.  I was going throug ...
reads bam mate written 4.9 years ago by thecuriousbiologist430 • updated 4 months ago by Pierre Lindenbaum120k
8
votes
1
answer
7.0k
views
1
answer
Ht-Seq Read Count And Strand-Specificity
... Hi, I am new to RNA sequencing and I am a bit confused with the HT-Seq read count options and I want to know whether I am thinking in the right direction. I have a set of paired-end strand-specific RNA-Seq reads and I am now trying to count the reads in a set of features (genes). The HT-Seq doc ...
htseq read rna counts strand written 6.1 years ago by thecuriousbiologist430 • updated 6.1 years ago by Ido Tamir5.0k
3
votes
2
answers
3.2k
views
2
answers
Concordance Between Ngs Snp Calls And Genotype Snp Arrays
... Hello, The accuracy of NGS SNP calls is usually determined by calculating concordance between these NGS SNP calls and the SNP array data (which is known to call the true SNPs). Are there any tools out there that calculate this concordance ? Any thoughts and suggestions would be much appreciated. ...
array ngs genotype snp written 6.1 years ago by thecuriousbiologist430 • updated 6.1 years ago by aindap110
1
vote
3
answers
6.3k
views
3
answers
Answer: A: Question : Plotting Per Chromosome/All Chromosome Coverage From Ngs Bam File
... When Qualimap reports the per chromosome mean coverage, does it normalize by the size of the chromosome ? I have certain chromosomes where I always get a low coverage as compared to others ? ...
written 6.2 years ago by thecuriousbiologist430
0
votes
3
answers
6.3k
views
3
answers
Comment: C: Question : Plotting Per Chromosome/All Chromosome Coverage From Ngs Bam File
... Thanks. Yes, I did finally move on to Qualimap. I ran it on some small datasets and the reports look good. ! ...
written 6.2 years ago by thecuriousbiologist430
5
votes
3
answers
6.3k
views
3
answers
Question : Plotting Per Chromosome/All Chromosome Coverage From Ngs Bam File
... Hi, I wish to plot per chromosome coverage from a BAM file obtained from aligning exome sequencing data. Are there any good R packages/any other non-R packages that can quickly get me such plots ? I was planning to use samtools to generate pileup files and then go on from there, however that wo ...
chromosome coverage plot written 6.2 years ago by thecuriousbiologist430
10
votes
2
answers
2.9k
views
5 follow
2
answers
Plotting Exon Statistics In R
... Hi, I have a table in the following format which provides some information (counts of mapped reads) about exons in some genes across some samples. Exon Gene sampleA sampleB sampleC E1 A 43 52 12 E2 A 0 24 34 ...
R exon written 6.3 years ago by thecuriousbiologist430 • updated 6.3 years ago by Dan500
14
votes
4
answers
17k
views
13 follow
4
answers
Calculate Per Exon/Per Gene Coverage
... Hi, I have a list of exons (in BED format) and I wish to find the coverage per exon from a BAM file. I was looking at Bedtools coverageBED but I don't think that gives me the per exon coverage. Are there any suggestions on how I should go about calculating the coverage of each exon ? Also, eve ...
gene exon coverage written 6.4 years ago by thecuriousbiologist430 • updated 6.4 years ago by biorepine1.4k

Latest awards to thecuriousbiologist

Popular Question 4.4 years ago, created a question with more than 1,000 views. For Fastq Quality Read And Score Length Check
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Fastq Quality Read And Score Length Check
Great Question 4.8 years ago, created a question with more than 5,000 views. For How To Find Major And Minor Alleles From Dbsnp ?
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Question : Plotting Per Chromosome/All Chromosome Coverage From Ngs Bam File
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Which Column Of A Vcf File Indicates The Reference Allele?
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Fastq Quality Read And Score Length Check
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Calculate Per Exon/Per Gene Coverage
Popular Question 5.7 years ago, created a question with more than 1,000 views. For How To Find Major And Minor Alleles From Dbsnp ?
Student 5.7 years ago, asked a question with at least 3 up-votes. For Plotting Exon Statistics In R
Student 5.7 years ago, asked a question with at least 3 up-votes. For How To Find Major And Minor Alleles From Dbsnp ?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1093 users visited in the last hour