User: colin.kern

gravatar for colin.kern
colin.kern180
Reputation:
180
Status:
Trusted
Location:
United States
Last seen:
2 months ago
Joined:
5 years, 9 months ago
Email:
c*********@gmail.com

about me

Posts by colin.kern

<prev • 42 results • page 1 of 5 • next >
0
votes
0
answers
152
views
0
answers
Comment: C: How can I figure out the NCBI annotation version of a GFF file?
... The reviewers have asked me to include the annotation releases version, so unfortunately this isn't just a matter of convincing myself it doesn't make a difference to the analysis. I agree that the annotation versions shouldn't be significantly different within the same genome build, however the gen ...
written 9 weeks ago by colin.kern180
0
votes
0
answers
152
views
0
answers
How can I figure out the NCBI annotation version of a GFF file?
... I am writing a manuscript for a study that used the NCBI annotations for the chicken, cattle, and pig genomes. The analysis was performed over a year ago using the current annotations for those species, however they have all been updated on NCBI since. As far as I can tell the annotation release ver ...
genome rna-seq written 9 weeks ago by colin.kern180
1
vote
1
answer
179
views
1
answers
Answer: A: Assessing chIP-seq plotfingerprint IP strength
... The R1 input definitely looks like it was not sequenced deeply enough. You can see from the graph that it seems like about 40% of the genome has no reads at all. As for whether you got non-specific binding for the IP libraries, that's harder to determine. The curves you have can be ok for broad hist ...
written 10 weeks ago by colin.kern180
2
votes
1
answer
253
views
1
answers
Answer: A: Quick Way to Annotate a Bed File
... bedtools intersect should be the solution, but the chromosome names need to match between the files and in what you posted you have "Chr1" for one and "chr1" for the other, so it won't find any intersections as it sees those as completely separate chromosomes. With that fixed, this command should wo ...
written 12 weeks ago by colin.kern180
0
votes
0
answers
146
views
0
answers
Finding SNPs between two inbred genetic lines
... I have DNA sequencing from two highly inbred genetic lines of chicken, so I expect them to be almost entirely homozygous. I'm interested in getting a VCF file of the SNPs that exist between these two lines. It seems like there are two ways I can do this using GATK: 1) Run GATK twice, once on the da ...
snp written 12 weeks ago by colin.kern180
0
votes
2
answers
426
views
2
answers
Comment: C: Using UCSC Genome Browser with results from NCBI or Ensembl assemblies
... Thanks. Do you know what resources were used to make those mappings? I work with farm animal species and none of them are on that Github. ...
written 9 months ago by colin.kern180
2
votes
2
answers
426
views
2
answers
Using UCSC Genome Browser with results from NCBI or Ensembl assemblies
... If I want to display some data on the UCSC genome browser, but have done the analysis with the Ensembl or NCBI assemblies and annotations, do I need to manually write scripts to replace all the chromosome IDs with the UCSC genome browser ones? It seems like this would be a very common situation that ...
ncbi ensembl ucsc browser written 9 months ago by colin.kern180 • updated 9 months ago by Emily_Ensembl16k
1
vote
1
answer
1.1k
views
1
answer
What exactly is the denominator when normalizing expression for sequencing depth?
... I have a question about the calculation of RPKM/FPKM and TPM in regards to how they are normalized for sequencing depth. I can think of at least 3 numbers that could be use as the denominator when doing this normalization: the total number of raw reads, the total number of raw reads that successfull ...
rna-seq written 12 months ago by colin.kern180 • updated 12 months ago by Devon Ryan85k
4
votes
3
answers
1.8k
views
6 follow
3
answers
Why estimate fragment size of ChIP-seq with SPP when using Macs2 for peak calling?
... I've noticed that most of the major projects involving wide-scale ChIP-seq analysis like ENCODE and Blueprint use a pipeline that involves running the SPP peak caller to estimate fragment size, then using Macs2 to do the peak calling but with the "--no-model" flag and giving Macs the fragment size e ...
chip-seq written 20 months ago by colin.kern180 • updated 20 months ago by EagleEye5.7k
1
vote
4
answers
1000
views
4
answers
Answer: A: Please, please, define what a 'read' is.
... Reads are definitely not fragments. For most assays, you are going to have fragments much bigger than the size of your reads. If you did single-end sequencing, you will extend all aligned reads to your predominant fragment size (hopefully you did size selection), or if you did paired-end reads you c ...
written 23 months ago by colin.kern180

Latest awards to colin.kern

Scholar 12 weeks ago, created an answer that has been accepted. For A: Quick Way to Annotate a Bed File
Great Question 7 months ago, created a question with more than 5,000 views. For Can't convert paired end BAM to bed using bedtools
Popular Question 7 months ago, created a question with more than 1,000 views. For vcf-consensus Error: Fasta sequence does not match REF
Popular Question 7 months ago, created a question with more than 1,000 views. For Tophat align_summary.txt and samtools flagstat accepted_hits.bam disagree
Popular Question 7 months ago, created a question with more than 1,000 views. For ChIP-seq Genome Coverage
Popular Question 7 months ago, created a question with more than 1,000 views. For Get # of unique mapped reads from Tophat output
Popular Question 16 months ago, created a question with more than 1,000 views. For Get # of unique mapped reads from Tophat output
Student 23 months ago, asked a question with at least 3 up-votes. For Get # of unique mapped reads from Tophat output
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools
Student 2.3 years ago, asked a question with at least 3 up-votes. For Get # of unique mapped reads from Tophat output
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1908 users visited in the last hour