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De novo alignement with smrttools

alignment smrttools denovo written 7 months ago by pablo • 160

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Difference SMRTlink / SMRTtools

smrttools pacbio smrtlink written 6 months ago by pablo • 160 • updated 6 months ago by GenoMax ♦ 95k

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installing SMRTtools 7 on MacOS error

smrttools pacbio written 8 months ago by Tatyana.sysoeva • 0 • updated 8 months ago by ATpoint ♦ 44k

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Recent Replies

C: How to create interval list from reference fasta or dict file? by MatthewP • 850
Ok, I already created this dict file, but don't know this can serve as interval list, thanks.
A: How to create interval list from reference fasta or dict file? by devarora • 310
Use picard tool java -jar picard.jar CreateSequenceDictionary \ R=reference.fasta...
A: How to specify samples for GATK FastaAlternateReferenceMaker in the option --use by Buxus • 0
An alternative is to maybe use [bcftools][1] consensus. [1]: http://samtools.github.io/bcfto...
C: Find sequences in a fast files present in another fasta file by rpolicastro ♦ 3.2k
Do the sequences match exactly? Also, is there any match in the names?
C: Salmon BAM target length different to FASTA file sequence length by Rob ♦ 4.6k
Hi [bdy8](https://www.biostars.org/u/52462/), Thanks for your detailed follow up! I am not su...
C: Error in converting the probsets by A • 3.9k
Sorry You are right This is the right one `GSE2457` I put CELL files from GSE2457 in rawdata d...
A: Historical Genbank genome assemblies missing? by GenoMax ♦ 95k
Archived human genome assemblies can be found at this [**NCBI FTP**][1] link. [1]: ftp://ftp....
C: Error in converting the probsets by Kevin Blighe ♦ 69k
No, GSE43700 is definitely human data, not rat. Please check the GEO record: https://www.ncbi.nlm...
A: Single cell RNA-seq anlaysis by jared.andrews07 ♦ 8.4k
To add to [rpolicastro](https://www.biostars.org/u/72027/)'s excellent answer, Bioconductor has t...
C: Error in converting the probsets by A • 3.9k
Thank you Yes this is Rat and as this is a public data this is my R object https://www.dropbox....
C: Error in converting the probsets by Kevin Blighe ♦ 69k
Thank you. You said that it is Rat?; however, the GEO record indicates that it is human. Can you ...
C: Error in converting the probsets by A • 3.9k
Thank you > featureNames(filt_eset2) [1] "1399067_at" "1388081_at" "1375569_at...

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