danshu

Actually I run falcon in a new directory in local mode.

Thanks for your explanation! Because I'm using FALCON-integrate 0.63/0.64, so has this been fixed in 0.7.1 or should I just use master branch of FALCON-integrate?

Hi, Can I ask some related questions? For diploid genomes, since we want to have a final haploid assembly, merging the p_ctg and a_ctg files before correction and scaffolding will...

Thank you so much for your explanation! @rhallPB

Thanks for your explanation! @pb-jchin So for the first question, do associated contigs with -02 suffix such as "001529F-001-02" correspond to second alternative paths of that bubble?

For bubbles having two alternative paths, then there must be assembly errors (e.g. caused by segmental duplication?) for a diploid genome? How do falcon and falcon_unzip deal with these bubbles?

I checked the quality scores of 1 read before and after error correction. Before: 33AAA/FBCEGGGEFGGGGGGGGFFGF:FFFFGG>FGGGGED@1FG1=C/FGGC@FFBFF@C

It seems that the quality scores of most bases were lower after error correction.

I have the sample question. After checking the script (https://github.com/Teichlab/cellphonedb/blob/master/cellphonedb/src/plotters/R/plot_heatmaps.R), this count is actualy the sum of all interactions between two cell types (e.g. CD8|NK + NK|CD8).

Since you are using Falcon, I assume you have a diploid genome to assemble. Quiver itself is not designed for diploid assembly so that the results of polishing diploid assembly...