Question: Having multiple adapter sequence in raw fastq files?
0
gravatar for mirzaei86.vahid
2.1 years ago by
mirzaei86.vahid30 wrote:

Dear all,

I have 50 RNA-Seq samples for a project. FastQC reports different TruSeq Adapter, Indexes (mostly 2, 7,5 and 14) for each of them and also some of them might have llumina Single End PCR Primer 1.

I see very good quality score (>30 for most of reads) but there were fluctuation in K-mer part (just like attached image), between bases 42-50. TruSeq Illumina indexes have 65 bases length however I found only 52 bases in reads. I have 2 question :

1- Should I treat each file bases on their overrepresented sequences? 2- How can I trim TruSeq-Indexes ( just those 52 bases)?

Thanks, Vahid

enter image description here

rna-seq next-gen • 1.0k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by mirzaei86.vahid30
1
gravatar for genomax
2.1 years ago by
genomax68k
United States
genomax68k wrote:

Use bbduk.sh from BBMap suite. BBMap includes all common adapters in a adapters.fa file that you will find in the resources directory when you download the software. It is ok to scan all of them at the same time against your data.

ADD COMMENTlink written 2.1 years ago by genomax68k

thanks @genomax2, how can I crop first 13 bases from start of reads??

ADD REPLYlink written 2.1 years ago by mirzaei86.vahid30
1

If this is RNAseq data then don't. See this post for an explanation.

If you still want to then check ftl= option for bbduk.sh.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax68k

thanks for your helps.

ADD REPLYlink written 2.1 years ago by mirzaei86.vahid30
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