Question: error for snp filtering
0
gravatar for mra8187
3.2 years ago by
mra818720
mra818720 wrote:

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
snp rna-seq software error • 854 views
ADD COMMENTlink modified 3.2 years ago by Pierre Lindenbaum129k • written 3.2 years ago by mra818720
0
gravatar for Pierre Lindenbaum
3.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Pierre Lindenbaum129k

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

ADD REPLYlink written 3.2 years ago by mra818720
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1727 users visited in the last hour