Question: Trimmomatic output explanation
0
gravatar for Mehmet
2.5 years ago by
Mehmet460
Japan
Mehmet460 wrote:

Dear All:

Input Read Pairs: 362047000 Both Surviving: 356436567 (98.45%) Forward Only Surviving: 4255577 (1.18%) Reverse Only Surviving: 1042122 (0.29%) Dropped: 312734 (0.09%)

here;

what do they mean?

Input Read Pairs:

Both Surviving:

Forward Only Surviving:

Reverse Only Surviving:

Dropped:

rna-seq sequence • 1.8k views
ADD COMMENTlink written 2.5 years ago by Mehmet460
3
gravatar for genomax
2.5 years ago by
genomax63k
United States
genomax63k wrote:

Selection criteria would be (for example but not limited to): length of the read, average quality of a group of bases etc. (post trimming)

Input Read Pairs: You started with these many read pairs

Both Surviving: Both reads R1/R2 survived trimming (met criteria you selected)

Forward Only Surviving: Only R1 read kept (R2 failed one or more selection criterion after being trimmed)

Reverse Only Surviving: Only R2 read kept (R1 failed one or more selection criterion after being trimmed)

Dropped: Neither R1/R2 pair satisfied selection criteria and were entirely were removed

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by genomax63k

Thank you very much.

ADD REPLYlink written 2.5 years ago by Mehmet460

are these results reasonable? After trimmomatic, I used Trinity for transcriptome assembly. I just want to be sure.

ADD REPLYlink written 2.5 years ago by Mehmet460

With just the numbers posted above to work with I would say they are.

ADD REPLYlink written 2.5 years ago by genomax63k
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