Question: repeatmasker file analysis
0
gravatar for AAK85
2.2 years ago by
AAK850
AAK850 wrote:

Hi I am new to bioinformatics. I have a command that I don't know what the output file will be? Can anyone help me understand the command? I don't know what the system does in the command line.

awk -F "\t" '{printf $0 "\t"} {system("samtools view -F 0x100 chr1.bam " $6 ":" $7"-"$8 "|" "wc -l")}' chr1RPTS > final.txt

the chr1RPTS is a file in repeatmasker format.

sequencing • 673 views
ADD COMMENTlink modified 2.2 years ago by genomax69k • written 2.2 years ago by AAK850
1

Output file will be called final.txt, if the command works as written (and as advertised). Are you getting anything in the final.txt when you run this command?

ADD REPLYlink written 2.2 years ago by genomax69k

Hi Yes. In my ch1RPTS file I have 17 columns and after this command my final.txt file has 18th column. I don't understand what the 18th column represents? Generally, in the repeatmasker file there are 17 columns, executing the {system("samtools view -F 0x100 chr.bam .......")} command adds one more column to my output file and I can't figure it out what it is representing? my complete command is this: awk -F "\t" '{printf $0 "\t"} {system("samtools view -F 0x100 chr1.bam " $6 ":" $7"-"$8 "|" "wc -l")}' chr1RPTS > final.txt

ADD REPLYlink written 2.2 years ago by AAK850
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