User: colin.kern

gravatar for colin.kern
colin.kern150
Reputation:
150
Status:
Trusted
Location:
United States
Last seen:
2 months ago
Joined:
5 years, 3 months ago
Email:
c*********@gmail.com

about me

Posts by colin.kern

<prev • 37 results • page 1 of 4 • next >
0
votes
2
answers
260
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 3 months ago by colin.kern150
2
votes
2
answers
260
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 3 months ago by colin.kern150 • updated 3 months ago by Emily_Ensembl14k
1
vote
1
answer
447
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 6 months ago by colin.kern150 • updated 6 months ago by Devon Ryan78k
4
votes
3
answers
1.1k
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 14 months ago by colin.kern150 • updated 14 months ago by EagleEye5.0k
1
vote
4
answers
760
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 18 months ago by colin.kern150
0
votes
2
answers
1.7k
views
2
answers
Answer: A: ChIPseq - Identical peaks in IP and input samples
... You shouldn't expect your input to be flat. Due to various factors with the physical structure of the genome, you'll get more fragments in some places which is independent of your IP. By getting a set of control reads which are sheared but not IPed, peak calling programs can use it as background to ...
written 18 months ago by colin.kern150
0
votes
1
answer
629
views
1
answers
Comment: C: Does Cuffmerge discard single-exon transcripts?
... You are correct, those genes are there. I forgot to mention that I have filtered out all transcripts with class_code "=" since I'm interested in finding novel long non-coding RNA. This leaves me with no single-exon transcripts. Could this be because cuffmerge "automatically filters a number of trans ...
written 20 months ago by colin.kern150
1
vote
1
answer
629
views
1
answer
Does Cuffmerge discard single-exon transcripts?
... I'm using cuffmerge to combine the transcripts built using cufflinks on different samples. I've just noticed that the annotation I get from cuffmerge contains no transcripts with only a single exon, they all have at least 2. Looking at the cufflinks output for the individual libraries, they do conta ...
cufflinks rna-seq written 20 months ago by colin.kern150 • updated 20 months ago by Satyajeet Khare1.2k
0
votes
1
answer
751
views
1
answer
Count Unique Alignments in BAM file
... I want to get the number of alignments in my bam file that aren't duplicates. I've run Picard Tools to mark duplicates on the bam file, but didn't use the option to actually remove them. I'd prefer not to rerun that step, but I can't figure out how to get a count of this. The samtools flagstat outpu ...
alignment rna-seq written 20 months ago by colin.kern150 • updated 20 months ago by geek_y8.4k
0
votes
1
answer
861
views
1
answers
Comment: C: vcf-consensus Error: Fasta sequence does not match REF
... I've added the vcf line to my post. ...
written 21 months ago by colin.kern150

Latest awards to colin.kern

Popular Question 10 months ago, created a question with more than 1,000 views. For Get # of unique mapped reads from Tophat output
Student 18 months ago, asked a question with at least 3 up-votes. For Get # of unique mapped reads from Tophat output
Popular Question 19 months ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools
Popular Question 20 months ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools
Student 22 months ago, asked a question with at least 3 up-votes. For Get # of unique mapped reads from Tophat output
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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1931 users visited in the last hour