User: colin.kern
colin.kern • 930
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Posts by colin.kern
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... From my understanding, if an annotated gene from Ensembl, UCSC, etc. is marked as being on the positive strand, that means its sense strand is the exact sequence from the assembly fasta file, and so the mRNA sequence is a copy of the genome assembly sequence for the exon regions (except with uracil ...
written 3 months ago by
colin.kern • 930
• updated
3 months ago by
swbarnes2 ♦ 8.9k
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Answer:
A: Enrichment Analysis in DAVID
... I have always just used the default background for the species. DAVID can be slow and unstable so I'm not surprised you're having trouble uploading a list of 15000. On a different note, I would reconsider whether it makes sense to do a GO term analysis separately on up-regulated and down-regulated g ...
written 6 months ago by
colin.kern • 930
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... I mostly work with single-end ChIP-seq, so I can't say much about some of your observations. For the Input getting a lot more reads than the IP, did you pool them on a single lane or sequence them separately? If pooled, did you just combine equal volumes or did you measure the concentrations and poo ...
written 7 months ago by
colin.kern • 930
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... You said this particular histone mark can cover up to megabases of the genome, so I would put more importance on the percentage of the genome covered by your peak calls, rather than just the number of peaks. All that Macs2 does to call broad peaks is to first call narrow peaks, then to combine nearb ...
written 7 months ago by
colin.kern • 930
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... You could downsample your input, i.e. randomly remove reads until it's the same depth of the ChIP. Try the plotFingerprint command of deepTools to graph the distribution of reads and see how the ChIP libraries compare to the input. Have you tried using a peak calling tool designed for broad histone ...
written 7 months ago by
colin.kern • 930
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... If the vast majority of your log2 ratios are negative, that means most of the genome has higher depth of the input compared to the ChIP library. Generally the SES scaling method is recommended when normalizing an input and ChIP, but I don't have experience with using it for very broad marks, so I'm ...
written 7 months ago by
colin.kern • 930
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... I have a set of short sequences obtained from doing DNase footprinting and I want to filter them by removing sequences that don't contain a known TF motif. I have done this with FIMO but we have decided to use Homer for doing motif enrichment rather than MEME, so I want to do the filtering with Home ...
written 7 months ago by
colin.kern • 930
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... The clustering can be different each time with kmeans if the initial cluster centroids are chosen randomly. I don't see any information in the deepTools documentation about what initializing method is used, but based on your results it seems like they may be assigned randomly. You can try a differen ...
written 8 months ago by
colin.kern • 930
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... > He had mentioned that since the amount of ncRNA varies from sample to
> sample, special care has to be taken to normalize for that. The
> samples were depleted for ribosomal RNA, but he said that there would
> still be a lot of rRNA in the samples, and this amount differs from
> one ...
written 8 months ago by
colin.kern • 930
1
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Answer:
A: Replacing BAM reference
... No, that won't work. It's not enough to just reheader because each alignment in the BAM file refers to a chromosome name defined in the headers, so if you're going to change the names in the headers, you need to go through each alignment and change the chromosome name there too. You'll need to know ...
written 8 months ago by
colin.kern • 930
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