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Hi all,
I am new to the field and I'd like to verify my variant calling pipeline using latest CHM13 as reference. I have the HG002v1.1.fasta here and I got the truth set v1.1.vcf from NIST.
> (ht…
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Hello,
I want to download the PacBio bam.
for example:
wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/CSHL_bwamem_bam_GRCh37/B…
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Hi, I ran this command to perform Isoquant quantification with the aim of obtaining transcript quantification results for all samples: isoquant.py --reference genome.fa --genedb ./merge.combined.gtf -…
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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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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
PacBio data is saved in BAM format and not in FastQ.
Is BAM supported and if not could it please be considered.
Converting 100's of GB BAM files to FastQ takes time and space and running directl…
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[svision-pro_germline_540201_4294967294.txt](https://github.com/user-attachments/files/16910625/svision-pro_germline_540201_4294967294.txt)
[test_hg002_pacbio_vacmap.zip](https://github.com/user-atta…
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I tried the program on PacBio hifi reads, which were for amplicon sequencing of some plant DNA samples, barcoded on both ends. The reason is that LIMA generated very simple report missing a lot of inf…
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Looking for insight/confirmation that Kaiju is operating as expected. My results thus far are suggesting that kaigu is misclassify reads that are very string BLAST hits to divergent taxa.
Specifica…