why is my txt file empty ?

Question

[zizigolu]

Sorry friends,

I tried to convert a sam file produced by tophat2 to txt but the output txt file is empty...why?

[izadi@lbox161 tophat_out]$ cat accepted_hits.sam |grep -v ^@| awk '{print $3}' > accepted_hits.txt

Any suggestion please? I need the txt file for biophysconnector package

I also tried another command with bed file but the output txt is empty again

cat file.bed | awk '{print $1}' > file.txt

Answer 1

[zizigolu]

actually both of used commands worked but the issue was that the first there was no gene id in first column in which i expect to be extracted then normally the produced txt file seemed empty!!! i donno why when i used bed produced from converting the tophat2 bam the txt file was empty while when used the bed from bowtie2, the txt file was not empty..

Answer 2

[James Ashmore]

TopHat outputs BAM files not SAM files - if you've converted the BAM file to a SAM file can you show me the command you used?

[zizigolu]

yes of course and the produced sam is not empty

the command:

[izadi@lbox161 ouput1]$ $SAM/samtools view -h accepted_hits.bam > accepted_hits.sam

do you know please how I can produce a txt file???? because I could display the average of reads by biophysconnector that needs two txt files from RNA-seq and ribo-seq and a bed file from ribo seq..then this package could extract the average of reads and show the graph...but I cant produce the txt file with sam nor bed

[James Ashmore]

Providing there are actual alignments in your BAM file and TopHat didn't encounter errors you should be able to do the following:

samtools view your_file.bam | awk '{print $3}' > your_file.txt

This will give you a text file with the name of the reference sequence that your reads aligned to

[zizigolu]

thank you,

I tried your command but the txt file is empty again

just one column

I
I
I
I
I
I

so on

[James Ashmore]

Can you show me a sample of your SAM file?

samtools view your_file.bam