B-1991-ing

Which minimum kmer is supposed to be used on the 701G merged single-end .fa reads?

1

Dear megabit support team, My two megabit command lines stopped after the 41 Hours running. Here, I pasted the error, log and command line of one running. Could you help...

Dear salmon support team, I firstly assembled MAGs from my metagenome data, then predicted the ORF gene operons using the prodigal software to generate the corresponding prodigal predicted MAG *faa...

Invalid genome ID: binny_XXXX_CXX_PXX_Actinobacteria[class]

2

Dear GTDB-Tk support team, I got the error - "**ERROR: The following characters are invalid: [ ) = ] ( ; ,**", due to my MAG name "binny_I01R01.000347_C91_P96_Actinobacteria[class].fasta" includes square...

Why the value of # scaffolds, # contigs, and Predicted genes are same?

2

Hi Matt, The column of **# Schaffolds** in my Chdb.csv file and my **Predicted genes** are the same. What went wrong there according to your experience? Best, Bing

Heatmap function always alphabetically plots the rows of the input matrix

2

Hi Zuguang, It is so strange that the Heatmap function doesn't give me the desired input row order when using the rowAnnotation. What I want is that it directly plots...

How to dealing with big gene dataset?

4

Dear cdhit development team, I have a big dataset. Because I predicted genes for each metagenome fasta using the prodigal software, then I got 16 prodigal annotated gene files, each...

Is it possible to get the full taxonomy for each taxid number of classified sequences?

3

Hi Derrick, Is it possible to get the full taxonomy for each taxid number of classified sequences? For example, the taxi 356? Best, Bing

Dear Karken support team, Why classified reads are contaminated reads? Is it due to the Kraken2 database a database made up of all possible contaminated bacteria? I used the Kraken2...

Is it possible to filter the kraken.report or bracken.report?

1

Hi Jennifer, So, is it possible for you to write a script to filter the taxonomy ids I need to generate a new kraken or bracken.report? I only want the...

No kraken2_translate.py after downloading the KrakenTools?

1

Hi Jennifer, No kraken2_translate.py in the downloaded KrakenTools folder, although it was merged into the main KrakenTools. Best, Bing