Hi, I'm new to RNASeq pipeline and biostars. So I apologize in advance if I say anything incomplete or incorrect.
For C.elegans , after downloading the index file via the link and unzip/untar, I ran the .sh file with the bash command. Then I ran the hisat code below.
For the single strand:
hisat2 \
-p 16 \
--rg-id=SRR006519 \
--rg SM:L3 \
--rg LB:SRR006519-L3 \
--summary-file SRR006519.txt \
--rg PL:ILLUMINA \
-x $RNA_REF_INDEX_NEW \
--dta \
--rna-strandness RF \
-u $RNA_DATA_TRIM_DIR_NEW/SRR006519.fastq.gz \
-S ./SRR006519.sam
For the reverse strand:
hisat2 \
-p 16 \
--rg-id=SRR360125 \
--rg SM:L3 \
--rg LB:SRR360125-DAUER \
--summary-file SRR360125.txt \
--rg PL:ILLUMINA \
-x $RNA_REF_INDEX_NEW \
--dta \
--rna-strandness RF \
-1 $RNA_DATA_TRIM_DIR_NEW/SRR360125_1.fastq.gz \
-2 $RNA_DATA_TRIM_DIR_NEW/SRR360125_2.fastq.gz \
-S ./SRR360125.sam
And I got the following error from both of them:
Error: Encountered internal HISAT2 exception (#1)
Then I tried to create index with hisat2-build by the following code:
hisat2-build -p 8 Caenorhabditis_elegans.WBcel235.86.fa Caenorhabditis_elegans.WBcel235.86
Here is the links for assembly and annotation files.
After re-running the same codes for single strand and reverse strand which is above, the code for reverse strand worked properly while getting the same error for single strand. I couldn't solve the problem, I would be grateful if you could help.
thank you very much everything is working fine now