Question: Fastq Joiner, "Bases to insert between joined reads"
0
gravatar for moriped
2.5 years ago by
moriped0
moriped0 wrote:

Hi,

In Fastq Joiner, how is the "Bases to insert between joined reads" determined?

Can it be left vacant?

Or can it be an arbitrary number like "400", if I know the library was made from 500bp fragments?

Many thanks in advance, Mike

rna-seq • 487 views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by moriped0
0
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Yes, this is a user defined setting that can be left empty on the tool form.

Perhaps try both for your analysis (no extra bases and values like 400 - or potentially test others). Map to see what produces the best mapping rates/positions.

Thanks, Jen, Galaxy

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson25k
0
gravatar for moriped
2.5 years ago by
moriped0
moriped0 wrote:

Hi Jen,

Thank you for your advice ! I will try it.

Best, Mike

ADD COMMENTlink written 2.5 years ago by moriped0
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