Average Coverage after Assembly (Spades)

Question

[davidmaimoun]

Hi, I would like to know to average coverage of my assemblies (gotten by spades). I ran bbmap to mapping my reads (the same ones I used to make the assembly) to the assembly. But I am not really sure that is the way and the answers on the different forums didn't completely help.

Command

bbmap.sh in=./trimmed/NM167_S34_R1.fastq in2=./trimmed/NM167_S34_R2.fastq ref=./assembly/NM167_S34.fasta covstats=covstats.txt

I got output like this:

#ID Avg_fold    Length  Ref_GC  Covered_percent Covered_bases   Plus_reads  Minus_reads Read_GC Median_fold Std_Dev

NODE_1_length_79421_cov_85.482448   261.1709    79421   0.5185  100.0000    79421   60378   60230   0.5259  253 111.34

....

I will really appreciate your help!

Thank you

[davidmaimoun]

I see now I got the average, but it's printed on the terminal and doesn't appear in the covstats.txt file

Average coverage: 164.398 Standard deviation: 155.626 Percent scaffolds with any coverage: 84.91 Percent of reference bases covered: 99.56

And I don't know how to set it in a file I tried with the redirect output ">" but it is not working

Any Idea ?

Thank you

Answer 1

[taniapsduarte]

Hi,

I'm running into the same issue. Did you make it work? Or did you find an alternative method? Thanks!

[Brian Bushnell]

Answered below your post.

Answer 2

[Brian Bushnell]

bbmap.sh in=./trimmed/NM167_S34_R1.fastq in2=./trimmed/NM167_S34_R2.fastq ref=./assembly/NM167_S34.fasta covstats=covstats.txt 1>screen.txt 2>&1

...will redirect the screen output. The screen output goes to stderr (2>) not stdout (1>).