error for snp filtering

Question

[mra8187]

Dear all i am using this script to SNP filtering and get error ... what 's wrong .. best regards

**bowtie-inspect -s /media/mra/4A3B44B64CA65A93/SNP/DATA/Genom/refrense_genome/Bowtie2/indexed-refrence.fa  | tail -n +4 | cut -f 2- > '/home/mra/Desktop/genome_size.txt' cat junctions.bed | bed_to_juncs | flankBed -g '/home/mra/Desktop/genome_size.txt' -b 1 | s lopBed -g '/home/mra/Desktop/genome_size.txt' -b 2 > '/home/mra/Desktop/windows.bed'** # my scipt

Error

cut: cat: No such file or directory
cut: junctions.bed: No such file or directory
Could not locate a Bowtie index corresponding to basename "/media/mra/4A3B44B64CA65A93/SNP/DATA/Genom/refrense_genome/Bowtie2/indexed-refrence.fa"
Command: bowtie-inspect --wrapper basic-0 -s /media/mra/4A3B44B64CA65A93/SNP/DATA/Genom/refrense_genome/Bowtie2/indexed-refrence.fa 
s: command not found

Answer 1

[Pierre Lindenbaum]

missing pipe or semicolon before cat:

not

... nome_size.txt' cat junctio ...

but something like

nome_size.txt' |  cat junctio

or

nome_size.txt' ;  cat junctio

furthermore:

not:

| s lopBed

but

| slopBed

[mra8187]

thanks a lot. now .. my problem is :

my script : bowtie-inspect -s indexed-refrence.fa | tail -n +4 | cut -f 2- > '/home /mra/Desktop/genome_size.txt' cat junctions.bed | bed_to_juncs | flankBed -g '/home/mra/Desktop/genome_size.txt' -b 1 | slopBed -g '/home/mra/Desktop/genome_size.txt' -b 2 > '/home/mra/Desktop/windows.bed'

error is :

cut: cat: No such file or directory cut: junctions.bed: No such file or directory Could not locate a Bowtie index corresponding to basename "indexed-refrence.fa" Command: bowtie-inspect --wrapper basic-0 -s indexed-refrence.fa