Question: miRNA seq trimming
0
gravatar for bioLife
4.6 years ago by
bioLife50
Sweden
bioLife50 wrote:

I am analyzing miRNA sequencing data derived from a typical Illumina protocol for small RNAs. The problem is that although I have trimmed the reads for the adaptors, there are a lot of reads with length longer thatn 26bp.

What are these long reads? Should I trim the reads for hairpin sequence too? What's been actually sequenced? Else, what are the steps needed before alignining the reads to the reference sequence?

many thanks


 

mirna trimming ngs • 2.4k views
ADD COMMENTlink modified 4.6 years ago by Devon Ryan90k • written 4.6 years ago by bioLife50

which species? I have found a lot of tRNA, that could or couldn't be functional. If you are interested to know what they are, just map to ncrnadb, and see what are the longer reads. But if not, just follow Devon advice. Just make sure it happens the same everywhere.

ADD REPLYlink written 4.6 years ago by Lorena Pantano360
3
gravatar for Devon Ryan
4.6 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

There's more than just miRNAs in a typical smallRNAseq experiment. You'll also have piRNAs, snRNA, snoRNAs, and so on. If all that you care about are the miRNAs, then just focus on them and ignore the rest.

ADD COMMENTlink written 4.6 years ago by Devon Ryan90k
1
gravatar for Manvendra Singh
4.6 years ago by
Manvendra Singh2.0k
Berlin, Germany
Manvendra Singh2.0k wrote:

######## First step is to trim your file quite carefully, I do it with Cutadapt

/usr/local/bin/cutadapt --discard-untrimmed --minimum-length="Number" --maximum-length="Number" -a <adapter_sequence> In_seq.fastq > your_trimmed_file.fastq

###### then remove also the reads mapping to ribosomal and tRNA sequences 

bowtie --seedlen=23 --un output_file.fastq /path_to/bowtieindex/r_tRNA your_trimmed_file.fastq > /dev/null

your output_file.fastq should look better to allign.

 

HTH

ADD COMMENTlink written 4.6 years ago by Manvendra Singh2.0k
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