error for snp filtering
1
0
Entering edit mode
7.0 years ago
mra8187 ▴ 20

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
RNA-Seq SNP software error • 1.4k views
ADD COMMENT
0
Entering edit mode
7.0 years ago

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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2360 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6