User: colin.kern
colin.kern • 170
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Posts by colin.kern
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2
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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 2 days ago by
colin.kern • 170
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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 2 days ago by
colin.kern • 170
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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 6 months ago by
colin.kern • 170
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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 6 months ago by
colin.kern • 170
• updated
6 months ago by
Emily_Ensembl ♦ 15k
1
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1
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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 9 months ago by
colin.kern • 170
• updated
9 months ago by
Devon Ryan ♦ 81k
4
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6 follow
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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 17 months ago by
colin.kern • 170
• updated
17 months ago by
EagleEye • 5.5k
1
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4
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872
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4
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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 21 months ago by
colin.kern • 170
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2
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2
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... 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.kern • 170
0
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1
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712
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... 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.kern • 170
1
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1
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712
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1
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... 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 ...
written 23 months ago by
colin.kern • 170
• updated
23 months ago by
Satyajeet Khare • 1.3k
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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 Is combining fastq files before running tophat the same as combining bam file output from tophat?
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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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