In this repository you can find some toy data that can be used to test the pipeline once it is cloned. The data was downloaded from SRA using the nf-core/fetchngs pipeline v1.12.0 and the following SRR ids:
SRR1045638
SRR536237
SRR620007
SRR536234
SRR641696
SRR1045641
SRR536238
SRR1045707
SRR620008
SRR536235
SRR641695
Then, the raw fastq files were preprocessed using the nf-core/methylseq pipeline v2.6.0. Finally, the bam and cov files produced by the pipeline were subsampled to retain only the first 100K bp of chr1 using respectively SAMtools v1.18 and awk:
# bam
samtools view -b <coordinated_sorted_bam> "chr1:1-1000000" > <output_bam>
#cov
zcat <cov_file> | awk '($1 == "chr1" || $1 == "1") && $2 <= 1000000' | gzip > <output_cov>
Finally, a part of these samples are used to build the reference atlas and the remaining samples are used as bulk samples to be deconvolved:
experiment,tissue,donor,sample,usage
SRX388734,Lung cells,STL001,SRR1045638,atlas
SRX388734,Lung cells,STL001,SRR1045641,atlas
SRX175350,Lung cells,STL002,SRR536237,atlas
SRX175350,Lung cells,STL002,SRR536238,bulk
SRX388743,Pancreas cells,STL002,SRR1045707,atlas
SRX175354,Pancreas cells,STL003,SRR620007,atlas
SRX175354,Pancreas cells,STL003,SRR620008,bulk
SRX175348,Sigmoid colon cells,STL001,SRR536234,atlas
SRX175348,Sigmoid colon cells,STL001,SRR536235,atlas
SRX190161,Sigmoid colon cells,STL003,SRR641696,atlas
SRX190161,Sigmoid colon cells,STL003,SRR641695,bulk