Kallisto mapping paired end

Question

[Dk]

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 \

[cpad0112]

does Mus_musculus.GRCm39.cdna.all.index exist 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:

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 

[Dk]

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!!

[cpad0112]

Got it. Remove space immediately after \.

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

[Dk]

it works!!! Thank you so muchhh!

[ATpoint]

Please show the error message, we cannot see your screen, nor read minds :)

[Dk]

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

[ATpoint]

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.

[Dk]

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.