Spike-In

[hamzaaitabbou96]

Hi,

I would like to use the spike-In (using the eption -spk).
Can you explain me more how to use it
What we need in input to use it?

[arunhpatil]

Hi @hamzaaitabbou96,

Experiments involving Spike-in reads/standard synthetic reads at different concentrations are sequenced as standards. So, your typical input FASTQ reads would contain these spike-in reads along with miRNAs and other small RNA reads which need to be quantified. An example (and much more discussion on spike-in with other user) has been described in detail in the following issue. If you have any further questions, please let us know.

#27 (comment)

Thank you,
Arun.

[hamzaaitabbou96]

Hi,
I have this index spike :

spike_1
UUGAUUCCCAAUCCAAGCAAG
spike_2
UACCAACCUUUCAUCGUUCCC
spike_3
UCCCAAAUGUAGACAAAGCA

I replaced spike-in data already indexed in miRge by the command bowtie-build,
when i saw the contents of it by the command bowtie-inspect, i got this

spike_1
GACCCAACCAAGCAAG
spike_2
ACCAACCCACGCCC
spike_3
CCCAAAGAGACAAAGCA

my question why there is a change in the sequences ? (U was deleted from the sequence)