Elementolab/small RNA-seq pipeline

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  • clean up raw files 
perl ~/PROGRAMS/SNPseeqer/SCRIPTS/casava1.8_merge_move_data_old.pl --dir="Sa*" --tgtdir=. --exec=1  --pe=0
  • remove adapters

If the adapters have been masked, eg by the core: 

for f in  s_*.txt.gz; do gr_5n "perl /home/ole2001/PROGRAMS/SNPseeqer/SCRIPTS/fastq_remove_N_adapters.pl $f" --name=rem$f; done

Otherwise use Smith-Waterman: 

for f in *.gz; do echo $f; gr_5n "/home/ole2001/PROGRAMS/SMITH-WATER/remove_miRNA_adapter -fastqfile $f | gzip >  $f.noadapt.gz" -name S$f   ;  done


  • Align reads 
for f in *.noadapt.gz; do PBS_quickAlign.pl --fastq=$f --bwaidx=/pbtech_mounts/oelab_scratch002/ole2001/DATA/GENOMES/hg19/hg19bwaidx --submit=1; done

Same for mouse 

for f in *.noadapt.gz; do PBS_quickAlign.pl --fastq=$f --bwaidx=/home/ole2001/PROGRAMS/SNPseeqer/REFDATA/mm9/mm9idx --submit=1; done


  • get a sample list 
perl ~/PROGRAMS/SNPseeqer/SCRIPTS/RNAseq_sampleinfo.pl --dirs=.  > sample_infos.txt

Typical output 

.       1       CA10S           GTGGCC  human
.       2       CA12S           GTTTCG  human
.       3       CA13S           CATGGC  human
.       4       CA14S           CATTTT  human
.       5       CA16S           CCAACA  human
.       6       CA1S            AGTCAA  human


  • run miRseeqer 
perl /home/ole2001/PROGRAMS/miRSeeqer/run_miRSeeqer.pl --samples=samples_info.txt --mir=1 --genome=hg19


  • run stats analysis 
perl ~/PROGRAMS/miRSeeqer/run_miRSeeqer_summarize_stats.pl --samples=sample_infos.txt


  • add sample group information, eg in a new file called sample_infos.txt.withgroups 
.       1       CA10S           GTGGCC  human     HCC
.       2       CA12S           GTTTCG  human     HCC 
.       3       CA13S           CATGGC  human     HCC 
.       4       CA14S           CATTTT  human     HCA
.       5       CA16S           CCAACA  human     HCA
.       6       CA1S            AGTCAA  human     HCA
  • to run a pairwise LIMMA analysis on all groups 
perl ~/PERL_SCRIPTS/expression_split_files_based_on_sample_info.pl --expfile=carcinoid_miRNA.txt --sampleinfo=sample_infos.txt.withgroups  --mirnas=1
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