Antônio Camargo

Wrong TPM values in 'transcript view' (sleuth_live)

11

I'm analyzing a transcript (TCONS_00028547) that's differentially expressed between two conditions. I've noticed that the TPM values that appear in sleuth live are different from the ones I get from...

Option to output gene-level abundances from sleuth_to_matrix, even when gene_mode = FALSE

9

I can't get gene-level expression values using `sleuth_to_matrix`, usig both `raw_obs` and `norm_obs`. The function returns a transcript-level matrix. I'm using version 0.30.0.

I added gene-level `obs_raw` support to `sleuth_to_matrix` by multiplying the normalized matrix by the size factors if the user request non-normalized values.

Puffaligner doesn't map read pairs to different references

2

Hi, There are some applications where it's important to identify reads pairs where the reads map to different references. Even though Puffaligner map reads independently ("(…) *we consider the chaining...

[Question] Effect of the 'genomicReads' parameter

1

Hey! I got one question: the `pufferfish align` command has a `--genomicReads` parameter, which I assume activates a non-splice alignment mode. However the README says that spliced-alignment is not currently...

[Suggestion] Allow output to stdout

2

Currently, the only way to get a bam file from puffalign is to write a sam and then convert it in a separate command. If puffalign could output to stdout...

Using more stringent parameters to avoid spurious sequences

9

Hey there, I've been testing some PLASS assemblies with my datasets and I noticed that it retrieves ~50x times more proteins than my MEGAHIT+Prodigal predictions, which is way more than...

Recurrently getting "Kmer matching step died"

7

I'm recurrently getting the "Kmer matching step died" error during my assemblies. I wasn't able to pinpoint what may be causing it because I sometimes get it and sometimes don't...

Core dump during assembly

2

My processes are constantly crashing in the middle of the assembly. I get a `*** glibc detected *** plass: invalid fastbin entry (free): 0x0000000000815a60 ***`. [plass.segmentation.log](https://github.com/soedinglab/plass/files/3653119/plass.segmentation.log) I installed Plass through...

Hey! kalign3 prints the log in stdout, which prevents users from redirecting it's output to a command that expects an alignment. One simple solution to this is to print the...