User: colin.kern

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colin.kern170
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Posts by colin.kern

<prev • 39 results • page 1 of 4 • next >
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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 2 days ago by colin.kern170
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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 2 days ago by colin.kern170
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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 6 months ago by colin.kern170
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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 6 months ago by colin.kern170 • updated 6 months ago by Emily_Ensembl15k
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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 9 months ago by colin.kern170 • updated 9 months ago by Devon Ryan81k
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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 17 months ago by colin.kern170 • updated 17 months ago by EagleEye5.5k
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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 21 months ago by colin.kern170
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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 21 months ago by colin.kern170
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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 23 months ago by colin.kern170
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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 23 months ago by colin.kern170 • updated 23 months ago by Satyajeet Khare1.3k

Latest awards to colin.kern

Scholar 2 days ago, created an answer that has been accepted. For A: Quick Way to Annotate a Bed File
Great Question 5 months ago, created a question with more than 5,000 views. For Can't convert paired end BAM to bed using bedtools
Popular Question 5 months ago, created a question with more than 1,000 views. For vcf-consensus Error: Fasta sequence does not match REF
Popular Question 5 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 5 months ago, created a question with more than 1,000 views. For ChIP-seq Genome Coverage
Popular Question 5 months ago, created a question with more than 1,000 views. For Get # of unique mapped reads from Tophat output
Popular Question 13 months ago, created a question with more than 1,000 views. For Get # of unique mapped reads from Tophat output
Student 20 months ago, asked a question with at least 3 up-votes. For Get # of unique mapped reads from Tophat output
Popular Question 22 months ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools
Popular Question 23 months ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools
Student 2.1 years ago, asked a question with at least 3 up-votes. For Get # of unique mapped reads from Tophat output
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Can't convert paired end BAM to bed using bedtools

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