lpantano · September 14, 2018 20:16
diff --git a/lossRand_3p_miraligner.sh b/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.
	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.