kwcurrin

Hello, Unless you want to use a peak caller specific to ATAC-seq, I would recommend using --shift -100 --extsize 200 because it is preferrable for fragments that span nucleosomes and...

The --shift -100 --extsize 200 option centers a 200 bp window on the Tn5 binding site, which is more accurate for ATAC-seq data (the same option is also applicable for...

Oh, I forgot to say I am using macs/2016-02-15

As an update, I wanted to make sure that the difference wasn't due to the Tn5 shift (+4 for + strand and -5 for - strand), so I reran the...

BEDTools correctly handles conversions between the 1-based GTF files and 0-based BED files. Is the start position of the intron (with the old leafcutter junction scripts) 0 or 1 based?...

Hello, Is it possible to obtain the beta-approximated p-values using the nominal p-value and the two shape parameters using the pbeta function in R? I tried this for my data,...

Hello, A colleague found out this issue results from different df values used in calculation of pval_beta and pval_nominal in analysisPermutation.cpp. The pval_nominal reported in the fastQTL output is calculated...

Hi Francois, Thank you for your response. It appears that annotate_outputs.py compares the nominal p-values (calculated with df) to the nominal p-value threshold (calculated with true_df). Is this correct? Would...