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lpantano/lossRand_3p_miraligner.sh

Created September 14, 2018 20:16
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lossRand_3p_miraligner
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lossRand_3p_miraligner.sh
Many sequences are not being capture in the current test_lossRand_3p.mirna. I don't know the reason, but following the instructions in how the authors generated this file I get different results.
```
wget https://github.com/lpantano/seqbuster/raw/miraligner/modules/miraligner/miraligner.jar
wget https://github.com/lpantano/java_seqbuster/raw/master/miraligner/DB/hairpin.fa
wget https://github.com/lpantano/java_seqbuster/raw/master/miraligner/DB/miRNA.str
java -jar miraligner.jar -sub 1 -trim 3 -add 3 -s hsa -i test_lossRand_3p.fastq -db . -o miraligner_lossRand_3p
# this sequences is not detected in the published data, but it is when you run this code.
grep -w TAAAGTGCTGACAGTGCAG miraligner_lossRand_3p.mirna
```
Actually this file has more than 6000 lines, whereas the file in this repo has only https://github.com/Gu-Lab-RBL-NCI/simulate-miRNA-reads/blob/master/Results/miraligner/no_pcr/test_lossRand_3p.mirna.
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