majiayu000 CLIP-seq Alignment
STAR Alignment
STAR --runMode alignReads \
--genomeDir STAR_index \
--readFilesIn trimmed.fq.gz \
--readFilesCommand zcat \
--outFilterMultimapNmax 1 \
--outFilterMismatchNmax 1 \
--alignEndsType EndToEnd \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix clip_
Bowtie2 Alternative
bowtie2 -x genome_index \
-U trimmed.fq.gz \
--very-sensitive \
-p 8 \
| samtools view -bS - \
| samtools sort -o aligned.bam
Post-Alignment Processing
# Index
samtools index aligned.bam
# Deduplicate with UMIs
umi_tools dedup \
--stdin=aligned.bam \
--stdout=deduped.bam
Related Skills
- clip-preprocessing - Prepare reads
- clip-peak-calling - Call peaks