User: colin.kern
colin.kern • 180
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Posts by colin.kern
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... 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.kern • 180
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... 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 ...
written 9 weeks ago by
colin.kern • 180
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... 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.kern • 180
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... 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.kern • 180
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... 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 ...
written 12 weeks ago by
colin.kern • 180
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... 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.kern • 180
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... 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 ...
written 9 months ago by
colin.kern • 180
• updated
9 months ago by
Emily_Ensembl ♦ 16k
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... 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 ...
written 12 months ago by
colin.kern • 180
• updated
12 months ago by
Devon Ryan ♦ 85k
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... 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 ...
written 20 months ago by
colin.kern • 180
• updated
20 months ago by
EagleEye ♦ 5.7k
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... 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.kern • 180
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For A: Quick Way to Annotate a Bed File
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For Can't convert paired end BAM to bed using bedtools
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For Get # of unique mapped reads from Tophat output
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For Can't convert paired end BAM to bed using bedtools
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For Can't convert paired end BAM to bed using bedtools
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For Can't convert paired end BAM to bed using bedtools
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