Output file with non-plastome reads?

[jdarias93]

Dear chloroExtractor Team,

I wanted to ask if chloroExtractor outputs a FASTA/Q file with the leftover reads that were not assembled in the fcg.fa file and, if so, what its called/how to access it. Thank you in advance.

[greatfireball]

Dear @jdarias93,

thanks for your interest in using chloroExtractor. Currently, we do not offer a special option to extract non-chloroplast reads from a sample set. But if more users require that feature, we would like to implemented in a future release. Nevertheless, you can use the output of chloroExtracter in combination with a mapper like bowtie2 to generate fastq files containing all not mapped reads. For example you can use the following commands to generate such a file set (I used Linux command line for that, hope that is okay for you):

# generate a mapping reference from the fcg.fa file
bowtie2-build fcg.fa chloroplast

# Map to chloroplast and ignore SAM output
# Reads which could not be mapped onto chloroplast should be written to 
# unmapped_concordantly.fq.1.gz and unmapped_concordantly.fq.2.gz
bowtie2 \
   --un-conc unmapped_concordantly.fq.gz \
   --threads 16 \
   -x chloroplast \
   -1 first_pair.fq \
   -2 second_pair.fq >/dev/null

Hope, that will solve your issue. In case you need it more than once, just let us know and will add it as new feature into one of our next releases.

Best,
Frank