Abhijit Sanyal

GLIBC ERROR

4

Hello, My conda environment is as follows active environment : ClusterEnv active env location : /mnt/common/rh6/annotate/Anaconda3/envs/ClusterEnv shell level : 2 user config file : /home/sanyalab/.condarc populated config files : /home/sanyalab/.condarc...

Creating a Hints file for use in Augustus from a gff file

6

Hi Jacques, The hintsfile in Augustus (https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md#using-hints) is a useful method of predicting genes. However, scripts are there to convert BAM (http://manpages.ubuntu.com/manpages/bionic/man1/bam2hints.1.html) and GTF files to the hintsfile (https://github.com/Gaius-Augustus/Augustus/tree/master/scripts). There...

Hello, Below is the command and error that I am getting while downloading species of Bradyrhizobium, and Leucobacter. Is this an issue on the ncbi side or the script? `(NCBIDownload)...

Hello, This is not a bug but a question. Can this tool be used to download cDNA and EST sequences in fasta format belonging to an Order, Class or Phyla?...

Hello All, This is NOT an Issue. I tried to get my question answered via gitter, but I have no response there. Therefore, I have to reluctantly post here. I...

Hello, This is not an issue but rather a question. I am using Augustus v2.7. After reading the manual I gave Augustus a repeat softmasked file, expecting the command to...

SNP Density Plot question on bin size

1

Hi, In the SNP_density plot I was not clear whether the bin-size parameter indicates overlapping window size or non-overlapping window sizes. If it is overlapping windows, then by how much...

Hello, You mention in the manual that the duplicate_gene_classifier tool should not be used on data from multiple genomes. I could not find the reason why in your paper. Is...

Use for plant mitochondria annotation

4

Hello, Can this software be used to annotate plant mitochondria as well? If so, any tweaks required in the software? What are the drawbacks in calling plant mito genes. Thanks...

agat statistics enhancement request

2

Hi Jacques, Instead of providing the average for a lot of features, can you provide the median, 90% and 95% percentile values? I feel these metrics summarize the annotation data...