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Thanks again for your help!
When using RNA-Bloom, I expected (perhaps naively) that the sum of `coverage of each contig X length of same contig` would not exceed the number of bases in my input dat…
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I'm not sure if I should be asking this here or on the `alevin fry` repo or here but anyway: I'm building a `spliceu` index and then using it for aligning a SPLiT-seq single nuclei (mouse) dataset. I'…
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Hi there,
I planned to use the pipeline for pacbio long-reads sequencing data. I have mapped the data using minimap2. Can I apply TEProf2 to TE finding? Thx in advance :)
Jianning
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Hi,
Thanks for your work, now we're trying to use Rasflow to process our RNAseq data.
In Rasflow, a transcriptome file (line 55 in config_main.yaml, TRANS: data/example/ref/transcriptome/Homo_sapien…
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Hi there,
I'm having an issue with bambu which I never had with version 2.2.0 and I was wondering if you could help me with it.
I have 4 different bam files (congtaining 4.4M, 4.75M, 356k, 26k ali…
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Is there a way you could make the output GTF file semantically compliant?
I get multiple error messages when using [AGAT gff2bed](https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gff2bed.…
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I'm not sure what format old Stringtie used, but Stringtie2 outputs a gtf file containing both the transcript locations and the quantities.
When I try the method suggested in the vignette, using i…
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Hello, I'm running bambu with just one bam file right now and got this error below when it got to the isoform quantification step. I have NaN somewhere but can figure out where. I also put what came b…
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1) Is there any filtering steps of reads going from the BAM alignment file to final transcriptome assembly. I.e. are some reads discards because they fail some QC filter like fraction coverage or read…
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Is it possible to get exon counts without summarising over genes or transcripts?
In addition, on [parameter reference](https://nf-co.re/rnaseq/3.8.1/parameters) webpage, the help for this parameter `…