Mark random reads that are mixed in by simulator in LRN (genome ID)

[sibyllewohlgemuth]

If random reads are generated by the read simulator (eg. CuReSim -r ) and these reads are marked in the read name of the original simulator, it would be nice if they would have a different genome ID in the RNF name.

[karel-brinda]

Could you provide a specific Snakefile that you are using in this case? CuReSim random reads are switched off in RNFtools, see this line. If you want to simulate contamination, it should be added through a separate source.

I could add a random mode option to rnftools.mishmash.CuReSim. Then your Snakefile could look like this:

# non-random reads
rnftools.mishmash.CuReSim(
       fasta=fa,
       number_of_read_tuples=10000,
       read_length_1=100,
       read_length_2=0,
)
# random reads
rnftools.mishmash.CuReSim(
       fasta=fa,
       number_of_read_tuples=2000,
       read_length_1=100,
       read_length_2=0,
       random=True,
)

[sibyllewohlgemuth]

Yes, exactly I wanted to mix in random contamination and i thougt I could do it with

rnftools.mishmash.CuReSim(
    fasta=fa,
        number_of_read_tuples=10000,
    read_length_1=100,
    read_length_2=0,
    other_params='-r 1000'
)

To have a random mode option would be useful! Then I can add the contamination through a separate source and it would have different genome ID.

[karel-brinda]

@sibyllewohlgemuth I added this feature, see the curesim_random branch. Could you check if it does what you expect? Thanks.

Example:

rnftools.mishmash.CuReSim(
    fasta=fa,
    number_of_read_tuples=10000,
    read_length_1=100,
    read_length_2=0,
)

rnftools.mishmash.CuReSim(
    fasta=fa,
    number_of_read_tuples=10000,
    read_length_1=100,
    read_length_2=0,
    random_reads=True,
)

[karel-brinda]

You can use the following command to install RNFtools from that branch:

pip install --upgrade https://github.com/karel-brinda/rnftools/archive/curesim_random.zip

[sibyllewohlgemuth]

Hi Karel, I tried the random mode and it does what I expected! Thank you!