CENTIPEDE.tutorial

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FIMO from the MEME suite website outputs data in the following format: motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence ZNF528 MA1597.1 Peak_31367#chr12#10213230#10213429 54 70 - 27.9633 1.45e-10...

Rosmaninho

Error in if (sum(idx) == 0) { : missing value where TRUE/FALSE needed

7

Hi, When I run the centipede_data , the result show : Error in if (sum(idx) == 0) { : missing value where TRUE/FALSE needed. Maybe it is some problem with...

zhuangfjnu

Error in quantile.default(x, c(TrimP, 1 - TrimP))

3

Hi, I use my own data to test the procedure, in the final steps, when I run: ```r idx 0.999 fit3

hugch2020

gunzip -c chr*.fa.masked > hg19.fa

5

Hello, When I run ``` gunzip -c chr*.fa.masked > hg19.fa ``` in [CENTIPEDE.tutorial](https://slowkow.github.io/CENTIPEDE.tutorial/) in Genomic sequence Section, I got the following error ``` gzip: chr10.fa.masked: not in gzip format gzip:...

zhenzuo2

About FIMO finding putative TFBS in the tutorial.

3

I read the CENTIPEDE manuscript. I think the author scanned all putative TFBS across the genome. However, in your tutorial, you suggested using FIMO only to obtain TFBS in peak...

alexyfyf