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Hi, thank you so much for the great tool.
I'm trying to apply longshot on long-read RNA-seq data (Iso-seq data from PacBio HiFi reads).
I ran the pipeline with default options and got ~30% reads …
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Hi ,
I would like to quantify the TE expression from pacbio iso-seq . I directly using minimap2 bam file to run TElocal using `--mode uniq`, but the ouput file all zero count. I would like to know it…
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Dear PBSIM3 maintainers,
I am YU Zhejian from the Zhejiang University-University of Edinburgh Institute. Our group has been using PBSIM1/2/3 to simulate long-read RNA-Seq reads (with [YASIM](https:…
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Hello @rrwick,
I experienced some poor mapping performance with Minimap2 for reads simulated using the pacbio2016 (only changing depth, mean sequence identity, all other settings as default). I notic…
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### Description of feature
I have downloaded subreads.fastq.gz file from SRR. I have tried Picard, sam-dump, reformat.sh to convert to unaligned.subreads.bam file so that I can run CCS.
However, see…
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1. SMART link user guide: https://www.pacb.com/wp-content/uploads/SMRT_Link_User_Guide_v10.1.pdf
2. Pacific Biosciences Glossary of Terms: https://www.pacb.com/wp-content/uploads/2015/09/Pacific-Bios…
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Hi @Magdoll ,
I created the environment and installed all the packages as per the tutorial.
I ran the following command:
`$ python sqanti_qc2.py --aligner_choice=minimap2 ~/pacbio/testdir/mapped.…
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Hi again,
I tried running MeShClust on 500 sequences that I simulated, all of length ~900nucleotides with most of the sequences highly similar (edit distances 1-20bp). A small portion of these sequ…
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Hi,
I wonder if bcctools also works correcting barcodes from 10x library followed by iso-seq instead of illumina seq? It would be nice if it works, since I am seeing a lot of unexpected barcodes in…
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Hi,
Is there documentation on how the CCS header file required for scallop-lr needs to be formatted?