I try to run and follow this tutorial https://www.bioinformatics.babraham.ac.uk/training/RNASeq_Course/Analysing%20RNA-Seq%20data%20Exercise.pdf but i got an error. Help me pls!
mfrlab:Desktop firdausraih$ hisat -x BP_index --known-splicesite-infile BP_splice_sites.txt -p 2 -U T1_1_d.fq, T1_2_d.fq, T2_1_Q30.fq, T2_2_d.fq, T5_1_d.fq, T5_2_d.fq, T6_1_d.fq, T6_2_Q30.fq | samtools view -bS - > BP_hisat.bam
-bash: samtools: command not found
Warning: Output file 'T1_2_d.fq,' was specified without -S. This will not work in future HISAT 2 versions. Please use -S instead.
Extra parameter(s) specified: "T2_1_Q30.fq,", "T2_2_d.fq,", "T5_1_d.fq,", "T5_2_d.fq,", "T6_1_d.fq,", "T6_2_Q30.fq"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/firdausraih/Desktop/hisat-0.1-2.6-beta/hisat-align-s --wrapper basic-0 -x BP_index --known-splicesite-infile BP_splice_sites.txt -p 2 -U T1_1_d.fq T1_2_d.fq, T2_1_Q30.fq, T2_2_d.fq, T5_1_d.fq, T5_2_d.fq, T6_1_d.fq, T6_2_Q30.fq
(ERR): hisat-align exited with value 1
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fatin nadhirah •
bash: samtools: command not found
This means that you have to install samtools
But it also looks like you have paired end data, for which you should use -1 and -2 rather than -U.
There is maybe also something wrong with the comma separated list with spaces.
I've already installed samtools and export the PATH but it still says command not found. What should i do?
i did but it still appear command not found :(
How did you install samtools?
Did you add the directory in which you installed samtools to $PATH? Check if everything is alright with
echo $PATH
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