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Hello everyone,
I just finished processing my Iso-Seq data and the pipeline I used, in brief, consisted of the isoseq3 steps, CD-HIT-EST followed by Cogent (using the CD-HIT outcome for this step) an…
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Good afternoon,
I performed PacBio iso-seq and after SQANTI3 filtering I quantified transcripts using RSEM-STAR.
I want to compare 3 cell populations and even after reading tappas paper/website an…
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Hello,
I'm running
```
$PASAHOME/Launch_PASA_pipeline.pl \
-c alignAssembly.config -C -R -g /home/zwl/data/Iso_seq/Gbi_Genome_NFU/Gbi_chr.fa \
-t LRSFmix.hq.fasta.clean -T -u LRSFmix.h…
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Does suppa2 apply to pacbio iso-seq ?
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Hi,
I am using longQC for my sequel II data and it ran fine in the past but currently, it is giving me errors for some samples and other samples are running fine.
The surprising thing is that all…
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We are getting the error "SeqClean on transcripts failed, check logfiles" for Pacbio hifi reads. Apart from the the error thare is notthing elase in the log files to locate issue. Thank you in advance…
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Hi sir
This link(ftp://brie4.cshl.edu/pub/pacbio_maize_B73/) is crashed.
I wanna download the data( 46,311 maize iso-seq transcripts from 11 developmental tissues that were filtered for intron r…
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Hello,
Thank you so much for creating this great tool! We're using it for annotating [ticks](https://github.com/czbiohub/tick-genome). I first heard about the tool from [Detlev Arendt](https://www.em…
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Commands for PacBio and ORF calling modules:
```
### Iso-Seq commands I ran in an interactive session on the UVA cluster:
### Input: jurkat.ccs.bam, NEB_primers.fasta, hg38.fa (for alignment)
…
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Hi,
I've been thinking about how to best process my IsoSeq data, and recently revisited the pages for best practices for mapping the reads to a genome (https://github.com/Magdoll/cDNA_Cupcake/wiki/Be…