Minor update in processing steps description.

Ribo-seq is still not up-to-date.

Data_submission/Data_submission.snakefile

@@ -98,6 +98,8 @@ paper = ref_info["paper"]
 submission_dir = ref_info["NCBI_submitter"]
 
 gather_processed_data = config.get("gather_processed_tables", False)
+if not gather_processed_data:
+    print("Only raw files will be gathered.")
 data_info = config["data"]
 LIBTYPES = list(data_info.keys())
 

Data_submission/libtype_info.yaml

@@ -94,7 +94,7 @@ Ribo-seq:
       The 5' and 3' 4 nt UMIs were removed from the trimmed reads using cutadapt (version 1.18) with options -u 4 and -u -4
       After removing UMIs, the reads from 28 to 30 nt were selected using bioawk version 20110810 (git commit fd40150b7c557da45e781a999d372abbc634cc21)
       The size-selected reads were mapped on the C. elegans genome (WBcel235) using bowtie2 (version 2.3.4.3) with options -L 6 -i S,1,0.8 -N 0
-      Mapped and remapped reads were used to estimate the abundance of structural RNAs using featureCounts (version 1.6.3) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
+      Mapped reads were used to estimate the abundance of structural RNAs using featureCounts (version 1.6.3) with options -O -s 1 --fracOverlap 1 and annotations corresponding to tRNA, snRNA, snoRNA, rRNA or RNA (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)
       The abundance of non-structural RNAs was estimated by subtracting the above counts from the number of mapped and remapped reads.
       Initially mapped reads were classified using a custom python program according to their length, composition and on the annotations on which they mapped. Reads that didn't match miRNA and piRNA annotations were considered as potential endo-siRNAs.
       The potential endo-siRNAs of size 21 to 23 nt that started with G were classified as \"si_22G\" if they mapped antisense to annotation belonging to the following categories: DNA transposons, RNA transposons, satellites, simple repeats (as annotated in http://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/rmsk.txt.gz) or pseudogene or protein-coding genes (as annotated in the iGenome distribution of WBcel235 obtained at ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Caenorhabditis_elegans/Ensembl/WBcel235/Caenorhabditis_elegans_Ensembl_WBcel235.tar.gz)