Question: A tool to cut off a certain length of nucleotide from reads
0
gravatar for s.kyungyong64
2.2 years ago by
Berkeley, USA
s.kyungyong6410 wrote:

Hi,

I have a genome of plant provided by a lab for me to assemble. This genome has Pac Bio and Illumina primer sequences that need to be removed beforehand. But I was told that some of the primers do not retain their full sequences, so instead of looking for the full sequences and trimming them out using software, they simply remove 70(?) nucleotide from both ends of every reads. Is this a better approach? And what tool would allow me to do this?

Thanks!

assembly • 777 views
ADD COMMENTlink modified 2.2 years ago by Brian Bushnell16k • written 2.2 years ago by s.kyungyong6410

Question: Trimming of partial adaptor sequences

ADD REPLYlink written 2.2 years ago by shenwei3564.5k
4
gravatar for cschu181
2.2 years ago by
cschu1811.6k
cschu1811.6k wrote:

In before Brian Bushnell suggests BBDuk. Use BBDuk: http://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/ >:D

ADD COMMENTlink written 2.2 years ago by cschu1811.6k

Oh, and I was so close, too!

ADD REPLYlink written 2.2 years ago by Brian Bushnell16k

Thank you! It's time to get back to bbduk then!

ADD REPLYlink written 2.2 years ago by s.kyungyong6410
2
gravatar for Brian Bushnell
2.2 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

At least for Illumina reads, that's a bad idea. Especially for libraries under 140 bp, since you'd have nothing left (but assembly would run very fast!)

PacBio libraries don't have read-end adapters like Illumina. Rather, they have "Smart Bell" adapters somewhere in the middle of the read. PacBio's software already removes those for you when creating filtered subreads. Sometimes it doesn't get all of them, so I wrote a tool to remove them removesmartbell.sh), but it's not normally necessary. Therefore for PacBio my recommendation is: Do nothing, though you can try running removesmartbell.sh if you are feeling adventurous or are interested in knowing whether there are any leftover adapter sequences.

For Illumina, you should do adapter-trimming as indicated here. You can also use BBDuk to forcibly trim the first and last 70bp from every read, but I don't recommend that in this case.

ADD COMMENTlink written 2.2 years ago by Brian Bushnell16k

Thank you for your helpful answer! I will follow your suggestion!

ADD REPLYlink written 2.2 years ago by s.kyungyong6410
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