Moderator: ATpoint

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ATpoint19k
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I hate Western blots.

Posts by ATpoint

<prev • 2,667 results • page 2 of 267 • next >
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Comment: C: Location of centromere
... Is it something well-annotated like human/mouse/fly/worm or a complete de novo assembly? ...
written 22 hours ago by ATpoint19k
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Comment: C: Which transcriptin factor bind to specific motif in mouse
... Yes, run TOMTOM :) What TOMTOM does is to take a sequence, here your `cgccgcc` and then compares it with all motifs you provide it, e.g. all TF motifs known in databases such as JASPAR or HOCOMOCO. If there is a significant similarity the tool will report it. That way you can check if your sequence ...
written 23 hours ago by ATpoint19k
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Answer: A: Which transcriptin factor bind to specific motif in mouse
... [TOMTOM][1] from the MEME suite can match a single sequence to a collection of PFMs which you can e.g. get from JASPAR or HOCOMOCO. [1]: http://meme-suite.org/doc/tomtom.html ...
written 1 day ago by ATpoint19k
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Answer: A: Whole Genome BiSulfite Sequencing and RRBS have 2bp coordiantes in output, how b
... BED files are 0-based. The output indicates a single base, see https://www.biostars.org/p/84686/ ...
written 1 day ago by ATpoint19k
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Comment: C: know the grep command for fastq file
... Hey https://www.biostars.org/u/11779/, thanks for contributing but please note that exactly this answer has already been given twice. There is no point in a third identical answer. ...
written 1 day ago by ATpoint19k
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Comment: C: Check for variation between two replicates in transcriptome data
... Pearson Correlation is a good start, so `cor` on the count matrix. What question do you eventually want to answer? ...
written 1 day ago by ATpoint19k
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Comment: C: Quantify expression from CAGE data
... You should state in which format you have the data. Fastq, Bam, count matrix... ...
written 3 days ago by ATpoint19k
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Comment: C: rnaseqcomp for own data withoutref genes
... Not helping with your question but you better compare recent tools such as kallisto to salmon rather than rsem which is quite old by now. For differences between salmon and rsem see e.g. https://www.biostars.org/p/237868/. You should also check the papers of these tools as they contain some benchmar ...
written 3 days ago by ATpoint19k
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Comment: C: Biological replicates and depth seq
... Any idea why these two "groups" exist, is this maybe a strong batch effect? This cannot be all based on seq. depth, I guess. ...
written 3 days ago by ATpoint19k
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Comment: C: Biological replicates and depth seq
... Can you show a PCA? plotPCA(rld, "condition", 1000) ...
written 3 days ago by ATpoint19k

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Teacher 4 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
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