add blacklists

assets/BLACKLISTS.md

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+# BLACKLISTS
+
+We provide both the ENCODE NGS blacklist as well as the merge of the ENCODE blacklist and the ATAC-seq blacklist for mitochondrial
+homologs in the genome.
+
+## Mouse
+
+```bash
+
+mkdir mm10
+
+# ENCODE:
+wget https://github.com/Boyle-Lab/Blacklist/archive/v2.0.tar.gz && tar zxf v2.0.tar.gz
+gzip -c -d Blacklist-2.0/lists/mm10-blacklist.v2.bed.gz | cut -f1-3  > ./mm10/mm10_encode_blacklist_v2.bed
+
+# Mitochondrial
+curl -o - -s https://raw.githubusercontent.com/buenrostrolab/mitoblacklist/master/peaks/mm10_peaks.narrowPeak \
+| cut -f1-3 \
+| tee ./mm10/mm10_mito_blacklist.bed \
+| cat - ./mm10/mm10_encode_blacklist_v2.bed \
+| cut -f1-3 \
+| sort -k1,1 -k2,2n \
+| bedtools merge -i - > ./mm10/mm10_combined_blacklist.bed
+
+```
+
+## Human
+
+```bash
+
+mkdir hg38
+
+# ENCODE:
+gzip -c -d Blacklist-2.0/lists/hg38-blacklist.v2.bed.gz | cut -f1-3 > ./hg38/hg38_encode_blacklist_v2.bed
+
+# Mitochondrial
+curl -o - -s https://raw.githubusercontent.com/buenrostrolab/mitoblacklist/master/peaks/hg38_peaks.narrowPeak \
+| cut -f1-3 \
+| tee ./hg38/hg38_mito_blacklist.bed \
+| cat - ./hg38/hg38_encode_blacklist_v2.bed \
+| cut -f1-3 \
+| sort -k1,1 -k2,2n \
+| bedtools merge -i - > ./hg38/hg38_combined_blacklist_v2.bed
+
+rm -r Blacklist-2.0 v2.0.tar.gz
+
+```

assets/adapter_fasta.fa

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+>TruSeq
+AGATCGGAAGAGC
+>Nextera
+CTGTCTCTTATACACATCT