---
title: "13-lncRNA"
output: html_document
---

Using kallisto to get count data for lncRNA...

Need fasta
Need .fq

Grab .fq files

https://gannet.fish.washington.edu/Atumefaciens/20220224_cvir_gonad_RNAseq_fastp_trimming/S12M_R1.fastp-trim.20bp-5prime.20220224.fq.gz



wget -r \
--no-check-certificate \
--quiet \
--no-directories --no-parent \
-P . \
-A *fq.gz \
https://gannet.fish.washington.edu/Atumefaciens/20220224_cvir_gonad_RNAseq_fastp_trimming/



Downloading lncRNA fasta

wget --no-check-certificate https://gannet.fish.washington.edu/Atumefaciens/20220217-cvir-lncRNA_subsetting/GCF_002022765.2_C_virginica-3.0_lncRNA.fa



Creating an index
```{bash}
/home/shared/kallisto/kallisto \
index -i ../data/GCF_002022765.2_C_virginica-3.0_lncRNA.index \
../data/GCF_002022765.2_C_virginica-3.0_lncRNA.fa
```



```{bash}
find ../data/*_R1.fastp* \
| xargs basename -s _R1.fastp-trim.20bp-5prime.20220224.fq.gz | xargs -I{} /home/shared/kallisto/kallisto \
quant -i ../data/GCF_002022765.2_C_virginica-3.0_lncRNA.index \
-o ../output/13-lncRNA-kallisto/{} \
-t 40 \
../data/{}_R1.fastp-trim.20bp-5prime.20220224.fq.gz ../data/{}_R2.fastp-trim.20bp-5prime.20220224.fq.gz \
2>&1 | tee ../output/13-lncRNA-kallisto/{}.out
```







