sunta3iouxos

in chip-seq paired mode is not used for MACS2

4

I dug a bit into the logs and I noticed that even if the data are paired-end MACS2 is not in paired end mode. I am feeding the --peakCallerOptions "-f...

continuation from #924, warnings.warn("fragmentSize.metric.tsv is empty, this sets

12

This is the error I encountered: ```bash ChIP-seq -d /mnt/c/AP01/bamSpikes -j 8 --local --useSpikeInForNorm --getSizeFactorsFrom genome --spikeinExt Chromosome --sampleSheet /mnt/c/AP01/bamSpikes/H3K36me3.tsv --windowSize 500 mm10_gencodeM19_spikes /mnt/c/AP01/bamSpikes/H3K36me3_chip_type.yaml mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/workflows/ChIP-seq/internals.snakefile:71: UserWarning: fragmentSize.metric.tsv is empty, this...

Hi, I am getting the following after finishing running succesfuly rgt-THOR. ``` mambaforge/envs/rgts/lib/python3.7/site-packages/rgt/Util.py:69: ResourceWarning: unclosed file self.config.read_file(codecs.open(data_config_file_name, "r", "utf8")) ResourceWarning: Enable tracemalloc to get the object allocation traceback mambaforge/envs/rgts/lib/python3.7/site-packages/rgt/Util.py:73: ResourceWarning:...

CUT&TAG with Genrich

2

Are there specific setting or CUT&RUN. This the MNAse approach. MACS2 is not working that well do to low background.

[Request] looping inputs for multiple ChIP-seq comparisons

1

If my samplSheet has more than 2 conditions CSAW fails. Is it possible to split the samples by condition so that CSAW will do a one to one comparison? example...

plotFinger fails due to insaficient wall time

6

Hi all, How can I increase the wall time for plotfinger from 6 to 24hrs? it constantly fails. and also does not properly shutdowns the commands. running the squeue there...

Hi all, I have not been able to find an appropriate ansewer in the readthedoc page, so could you please let me know how I can properly update to the...

server disconected

1

server keeps disconnecting as soon as I upload the csv file

Hi, how do you convert the DESeQ2 output to clusterprofile specific for running gsea? thank you in advace

"[Error] Cannot open input file : %s" % read_file

1

command used ./bs3-align -1 test_data/pair1.fq -2 test_data/pair2.fq -o WGBC -f sam -g reference_genome/genome.fa -d reference_genome/ error I got: File "bs3-align.py", line 149 print "[Error] Cannot open input file : %s"...