-
Hello,
I have been trying to figure out how to incorporate external spike-in normalisation factors to both single-end and paired-end ChIP-seq data for peak calling with MACS2.
I tried peak calli…
-
I have a few questions regarding the parameters used in the dynamic program:
1. For each block, it appears that you solve `nb_bdg_all * nb_bdg_abar` optimization problems, the former imposing an ov…
-
Hi!
I am getting this issue when running hichipper:
Tue Aug 13 15:22:36 EDT 2019: .yaml file detected
Tue Aug 13 15:39:59 EDT 2019: Performing hichipper-modified background peak calling
Tue Au…
-
Hello,
I am trying to run SEACR with an IgG control. I get the error:
```
++ awk '{s+=$3-$2; t++}END{print s/(t*10)}' M5aetxQ1x2qc7.auc.threshold.bed
awk: cmd. line:1: fatal: division by zero …
-
Hi there,
I'm trying to use MACS2 bdgdiff for my ATAC-seq differential peaks analysis. I want to compare the differential expression between T2D (Type 2 Diabetes) and ND(Non-diabetes, control) with…
-
I am working with custom fasta and custom bedgraph files so that my bedgraph file looks like the following:
```
BarcodeRep-TSS-chr10:92593086-92593236,+ 1 1 0.0
BarcodeRep-TSS-…
-
Hi, Add this WFS and add the featuretype bivalves (it's the only one):
http://si.icnf.pt:80/geoserver/BDG/atlas_bivalves_2007/wfs
QGIS can't add the layer and raises an error (its a server problem…
-
Hi, I am trying to call peaks using SEACR using the following parameter settings
./SEACR_1.1.sh treatement.bdg control.bdg norm relaxed out
but I am getting very few peaks for some comparison. I…
-
@heuermh
I am trying to use bdg-ga4gh-convert 'alignmentConverter' to map ( or maybe collect to array and map locally) an AlignmentRecordRDD.rdd to ga4gh JSON.
To do so, I need to create a new…
jpdna updated
7 years ago
-
Hi Rongxin,
SnapATAC is an awesome package for single cell ATAC-seq analysis. After peak calling by MACS2, I am wondering how can I generate the bdg or bigwig file of a subset of nuclei based on co…