Kallisto mapping paired end
Hello everyone, I am new to bioinformatics and i am trying to use kallisto to map paired end data. However, I got an error by running the command. So does anyone know what did I do wrong here? Thank you!
Here is my command:
kallisto quant \
-i Mus_musculus.GRCm39.cdna.all.index \
-o testoutputS72 \
16wks_HFDWT_hepatocyte_1_S72_L003_R1_001.fastq.gz \ 16wks_HFDWT_hepatocyte_1_S72_L003_R2_001.fastq.gz \
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Please show the error message, we cannot see your screen, nor read minds :)
Hi, here are the error messages: Error: kallisto index file missing Error: file not found
Error: paired-end mode requires an even number of input files (use --single for processing single-end reads) Error: need to specify output directory
Usage: kallisto quant [arguments] FASTQ-files
File not found -- does the index exist?
Also, is the last
\indeed present or is this a pasting error? It makes a new line but the command should stop there, so remove it.Yes, I change my command line with no \ but it still have the same error though. Also, I have my index file inside my folder but idk why it shows as not found and I keep having the same error.
does
Mus_musculus.GRCm39.cdna.all.indexexist in current directory? In addition, why are you using\twice in in the last line? They are not necessary. Try some thing like this after making sure that index and files are in current directory:Yes, the index exist in the current directory but idk why it keeps showing error in that part. Also, I tried to rerun the code again and it's still have the same error. I really appreciate you guys help though!!
Got it. Remove space immediately after
\.it works!!! Thank you so muchhh!