Issues about output result files

[SuiyueWestlake]

Hi,

I have downloaded some Chip-seq data from GEO, and want to analyze these data using chilin.

Previously, I have successfully installed chilin and analyzed some data. However, I can not get the same output files like before. I got the bigwig files and also the peak files last time. But I only got some quality control result this time.

Here is my command for this time. chilin simple -u suiyue -s mm9 --threads 4 -i TFAP4_KO -o TFAP4_KO_result -t SRR9621130.fastq,SRR9621131.fastq,SRR9621132.fastq -c SRR9621133.fastq,SRR9621134.fastq,SRR9621135.fastq -p narrow -r tf Here is my result files for this time.

However, I got much more information last time. Here is my command for last time. chilin simple --threads 4 -i WT_vs_Igg -o WT_vs_Igg -u suiyue -s hg38 -t "2FT_1.fq.gz,2FT_2.fq.gz" -c "1IgG_1.fq.gz,1IgG_2.fq.gz" -p both --pe And this is my result file for last time.

Thank you so much for your help!

Best, Yue

[qinqian]

Hi Yue,

Thank you for your feedback! Could you please check if the mm9 reference has been loaded into the reference folder?

Best, Qian

[SuiyueWestlake]

Hi Qian,

Thank you so much for your reply. It's been almost 2 years since I last used Chilin. So I was wondering where I should put the mm9 reference in? 😭

This is the folder of my conda environment for chilin.

Thank you so much again!

[qinqian]

Hi Suiyue,

Yes, please take a look at the documents here (http://cistrome.org/chilin/Installation.html#download-dependent-data-for-hg38-hg19-mm9-or-mm10), it should be a db folder under the source code, and reinstall with python setup.py.

Best, Qian