brantfaircloth
commented
5 years ago Hi James,
Although you can use phyluce with any types of probes (e.g. exon and not uce), i can't support the multitude of ways that people do this so you are largely on your own. That said, you would generally expect larger contigs than your probes if the probes match a larger contig that was assembled by a program like trinity. so, the probe looks like it matches to this large contig perfectly, and you get the large contig when you extract the matching contigs from the assembled contigs. that's the expected behavior.
Hello,
I ran my split contigs with exon probes working until getting fasta files below. The log file was completed well. I used min-identity=95; min-coverage=95; regex='(ex-\d+)(_chr\d+)(_s\d+)(_e\d+.*)'.
source activate phyluce
for i in {0..30} do phyluce_assembly_get_fastas_from_match_counts \ --contigs exon_contig8g_set2 \ --locus-db exon_contig8g_set2-exonprobe.${i}/probe.matches.sqlite \ --match-count-output exon_contig8g_exonprobe.${i}-taxa-incomplete.conf \ --output exon_contig8g_exonprobe.${i}-taxa-incomplete.fasta \ --incomplete-matrix exon_contig8g_exonprobe.${i}-taxa-incomplete.incomplete \ --log-path log done
PROBLEM: I saw my exon_contig8g_exonprobe.${i}-taxa-incomplete.fasta getting sequences larger than probe size & lastz results.
Ex.
my probe name: ex-1652 (181bp)
lastz (also 181bp; min-identity=95; min-coverage=95)
17236 >NODE_5776073_length_44302_cov_1933206 + 40935 41116 181 >ex-1652_chr10_s94852732_e94852913 - 0 181 181 ..................................................................................................................................................................................... 181M 181/181 100.0% 181/181 100.0%
exon_contig8g_exonprobe.0-taxa-incomplete.fasta
Could you please suggest me how this error happened? I like to make it work, as I am close to a final step now.
Thanks, James