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Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone

pbalign tutorial polishing pacbio arrow smrt limk written 8 months ago by Roxane Boyer • 530 • updated 3 months ago by elipow1 • 0

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561

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Help Needed with Pbalign SamFIlter

quiver pbalign pacbio samfilter written 17 months ago by anniiee9 • 0 • updated 17 months ago by Biostar ♦♦ 20

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416

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samFilter Shows CoreDump

quiver pbalign samfilter written 17 months ago by anniiee9 • 0

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526

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pbalign - SortService returned a non-zero exit status

assembly pbalign pacbio written 19 months ago by mjp • 10 • updated 18 months ago by Biostar ♦♦ 20

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pbalign issue: blasr v5.1 seems to be not integrated with pbalign

alignment pbalign blasr pacbio written 20 months ago by Pawel Osipowski • 20

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reference sequence for blasr and pbalign

de novo assembly pbalign blasr pacbio written 2.3 years ago by komwit.s • 0

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C: No QD scores on 10% of observations in VCF? by miles.thorburn • 10
Hi, Correct, you go through HaplotypeCaller, then GenomicsDBImport, and finally into GenotypeGVC...
C: Which HTSeq mode is suitable for RNAseq data to be used for differential gene ex by grant.hovhannisyan • 780
If you use STAR as mapper, you can specify the option `--quantMode GeneCounts` and STAR will outp...
C: extracting orphan reads from bam file by Assa Yeroslaviz • 1.1k
Thanks Pierre, I am not sure how to use this snippet to my needs. The bam file I have is the resu...
A: Which HTSeq mode is suitable for RNAseq data to be used for differential gene ex by h.mon ♦ 14k
As stated above, featureCounts is faster and probably equivalent or better than HTSeq. But to ans...
A: Biobase not running in R 3.5.0 by h.mon ♦ 14k
Check `.libPaths()`, probably the older Biobase is still installed and has precedence over the ne...
C: sciClone input, output and parameters by genomax ♦ 47k
Please don't post new questions as `answers` in existing threads. If it is truly a new question t...
C: QIIME filter_fasta.py not removing chimeric sequences by samanthabird • 0
Thank you both for your answers! I wasn't actually running through the QIIME pipeline, I had used...
A: sciClone input, output and parameters by sm.hashemin • 10
Dear people could sciclone handel multiallelic variants? if yes how should one make the input fil...
C: Sciclone clonevol integration by genomax ♦ 47k
Tagging: https://www.biostars.org/u/117/
C: Specific gene annotation for genome assembly by genomax ♦ 47k
It looks like annotated transcriptome data from a recent [Ambystoma mexicanum genome paper][1] on...
A: test if clustering differs by Kevin Blighe ♦ 19k
So, you have derived a gene signature of 400 genes that can seemingly segregate markers based on...
C: Bcftools view. FREQ inclusion error. by sm.hashemin • 10
Hi there try using the bcftools filter --include 'FREQ>0.1' inputfile.vcf --output outputfil...

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