Sowmya Parthiban

question on multisampling

8

I am trying the multisample mode, and running into out of memory issues which I expected to occur, but I can only assign a certain amount of RAM on my...

recommended quality control for input BAM files

1

Hi, I am just wondering if there is a recommended QC steps that is recommended for input bams? For e.g. recommended MAPQ threshold for minimap, removing supplementary reads, etc. ?...

Interpreting warning messages in discovery only mode

2

Hello, I have a bam file where my reads are aligned to the `GENCODE GRCh38.p14.genome.fa file`. The corresponding gtf file is `gencode.v44.chr_patch_hapl_scaff.annotation.gtf` I tried running BAMBU in discovery only mode...

Hi, I am getting this error in the final counts matrix generation step: does anyone know how to circumvent this issue? ``` b'[bam_sort_core] merging from 9 files and 12 in-memory...

I have a flagstat file here that looks like this: ``` flagstat 21384 + 0 in total (QC-passed reads + QC-failed reads) 14485 + 0 primary 6899 + 0 supplementary...

working with quantification tools that detect novel isoforms

1

For tools such as `bambu` and `isoquant`, they produce an extended gtf including the novel isoforms which are not accompanied by a fasta file containing the sequence information. Is the...

I have two conditions wherein for condition 1, a given set of isoforms for a gene are not expressed, and `iso_value = 0`. This in turn gets reported as `NaN`...

trying to understand the `OUT.novel_vs_known.SQANTI-like.tsv`

4

In the `OUT.novel_vs_known.SQANTI-like.tsv` file, are all the entries for novel transcripts? If so, I'm trying to wrap my head around why some of them are categorized as `FSM`. Any pointers...

read assignment information

4

Hi there, I am using `bambu 3.4.0` for quantification. I am curious about the read to transcript assignment, so I used the function mentioned in the document `metadata(se)$readToTranscriptMaps[[1]]`, but I...

Hi there, I am trying to understand how CPC2 analysis outputs are transformed into these categories on the switchplot. For both the `PTC` and `coding potential`, the values are either...