Jigyasa Arora

Thank you so much for a prompt reply @nick-youngblut! I will play with the LCA stringency score and completeness and contamination cut-off. I wanted to ask is redoing the taxonomic...

Thanks! I am testing it on a gut metagenome sample, will also let you know if there are huge differences or not. Thanks again for all the help!

Hey @nick-youngblut I compared the `ncbi-gtdb_map.py` script (hereafter called as method1) to taxonomy annotated via `gtdb_to_diamond.py` (hereafter called as method2) generated all_gtdb.faa file as a database. The results are very...

I went back to check the taxon ids assigned to gtdb accession numbers in accession2taxid.tsv generated via gtdb_to_diamond.py script. I think there is something wrong in the accession2taxid.tsv file. For...

Thanks for replying! I will use the older version.

Hi @wasade , Thank you for replying! I was using the most recent version of `sortmerna` in which the `indexdb_rna` is replaced with `indexdb`. But as recommended in the deblur...

Hi @wasade, Thank you for replying and sharing the qiita workflow link. I have a follow-up question, if I understand correctly. Qiita suggests using` fastp` for trimming followed by `deblur`....

Hey @cameronmartino I checked HumanN2 pipeline and they condense the beta-diversity distance matrix (Bray Curtis) by the sample mean to calculate "Contributional diversity". [code used-reduce_table.py, reference-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235447/#S12] I was wondering if...

Hi @milot-mirdita , Thank you for replying! I wanted to confirm another thing, while the E. values of the results are high, the alignment length of the match varies a...

Hi @milot-mirdita , I am comparing the output from Foldseek with hh-suite to find remote homologs, and I observe that none of the hits have E. values less than 1e-3....