Question: Problem with bad quality bases in RNAseq
0
gravatar for silas008
4.6 years ago by
silas008100
Brazil
silas008100 wrote:

Hi... I did a RNAseq to small RNAs (18-30nt). But the last (27-30) bases are with bad quality. Should I to cut that reads or not? I trimmed the last reads to obtain 18-25 reads and analized with this approuch but I dont know this is correct. 

rnaseq • 1.0k views
ADD COMMENTlink modified 17 months ago by Biostar ♦♦ 20 • written 4.6 years ago by silas008100
1

what is your read length? If it is long then you would cut the ends anyway. 

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 82k

Reads = 36nt. Shoul I cut the ends to obtain reads 18-30nt?

ADD REPLYlink written 4.6 years ago by silas008100

well if your reads are 36nt and 30 bases out of that are bad it will be a challenge to get useful information out regardless what you do. 

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 82k
1

I think he means base 27 onwards are bad quality. And yes, if they are bad quality you should trim, but if base 26 is good why did you trim it?

ADD REPLYlink written 4.6 years ago by h.mon29k

I see, I misread that section. There is no problem them ;-)

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 82k

Sorry. The bad quality scores are about 27 base, not exactly 27. But before 25 base I have very good quality scores.

ADD REPLYlink written 4.6 years ago by silas008100
0
gravatar for mark.ziemann
4.6 years ago by
mark.ziemann1.2k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.2k wrote:

Hi silas008, as a rule of thumb, you should be doing quality trimming (ie, fastq_quality_trimmer) then adapter clipping (fastx_clipper) before mapping small RNA reads.

ADD COMMENTlink written 4.6 years ago by mark.ziemann1.2k

Thanks, Mark!

Actually, I did that before do the mapping of my data. But the fastqc keeping shows some problems. But now I think I understand the fastqc reports for DNA, not for RNA. 

ADD REPLYlink written 4.6 years ago by silas008100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1619 users visited in the last hour