Discussions

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  Building salmon index

  MarkiMarki started Feb 16, 2022 in General

  

  

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  Forcefully gene quantfication with libtype "ISR" from unstranded library for Differential expression analysis

  daniazi asked Jan 29, 2022 in Q&A (bulk specific) · Unanswered

  

  

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  Why are some transcripts expressed at 0 in all samples, resulting in the count matrix having rows with all 0 values?

  ljyls asked Jan 29, 2022 in Q&A (bulk specific) · Unanswered

  

  

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  Issues with refgenie indexes

  SBaluszek asked Nov 12, 2021 in Q&A (bulk specific) · Unanswered

  

  

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  Any easier way to deal with quant files generated by different versions of Salmon

  sykbod asked Sep 20, 2021 in Q&A (bulk specific) · Unanswered

  

  

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  alevin library type for 10x Chromium v3

  deevdevil88 asked Jun 17, 2021 in Q&A (single-cell specific) · Unanswered

  

  

  

  

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  How Salmon deals with poly(N) in a genome/transcripts?

  ignadb asked Jul 19, 2021 in Q&A (bulk specific) · Unanswered

  

  

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  Salmon Compatibility with SLAM-Seq

  DKH12 asked May 4, 2021 in Q&A (bulk specific) · Unanswered

  

  

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  Alevin with 10x 5' v2

  JLTrincado asked Apr 16, 2021 in Q&A (single-cell specific) · Answered

  

  

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  alevin: the --whitelist flag

  eudoraleer asked Apr 8, 2021 in Q&A (single-cell specific) · Unanswered

  

  

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  Quantification output

  mavershang asked Feb 9, 2021 in Q&A (bulk specific) · Unanswered

  

  

  

  

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  Transcript orientation information to build index

  mriken asked Feb 15, 2021 in Q&A (bulk specific) · Unanswered

  

  

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  feature barcoding data (like CITE-seq) is taking too much time to process

  k3yavi asked Feb 12, 2021 in Q&A (single-cell specific) · Answered

  

  

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  Welcome to salmon Discussions!

  rob-p started Dec 9, 2020 in General

  

  

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  alevin: Almost no overlapping cell barcodes between GEX and HTO libraries

  ivanek asked Oct 20, 2020 in Q&A (single-cell specific) · Answered

  

  

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  alevin: Question related to noisy reads, whitelisting, and emptyDrops

  imranfanaswala asked Apr 14, 2020 in Q&A (single-cell specific) · Answered

  

  

  

  

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  alevin: is it possible to change order of UMI and CB in R1?

  DrHogart asked Mar 14, 2020 in Q&A (single-cell specific) · Unanswered

  

  

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