User: Lior Pachter

gravatar for Lior Pachter
Lior Pachter540
Reputation:
540
Status:
Trusted
Location:
United States
Website:
https://pachterlab.git...
Twitter:
@lpachter
Last seen:
6 months, 2 weeks ago
Joined:
5 years, 2 months ago
Email:
l*******@caltech.edu

Posts by Lior Pachter

<prev • 40 results • page 2 of 4 • next >
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Comment: C: Single-nucleus RNA-seq processing (10x) with Pseudoaligners (Kallisto)
... Unfortunately it's not that simple- bulk RNA-seq has reads from across transcripts and so quantification requires normalization by length. Having said that, if you are only interested in producing transcript compatibility counts then yes, this index can be used. ...
written 13 months ago by Lior Pachter540
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Answer: A: Single-nucleus RNA-seq processing (10x) with Pseudoaligners (Kallisto)
... There is a tutorial for how to do that here: https://github.com/BUStools/getting_started/blob/master/kallisto_bus_mouse_nuclei_tutorial.ipynb This is part of a series of tutorials for how to use kallisto | bustools for a variety of single-cell RNA-seq pre-processing tasks: [https://www.kallistobus. ...
written 13 months ago by Lior Pachter540 • updated 13 months ago by RamRS30k
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Comment: C: How to append R1(Barcode+UMI) to header of R2(Read data)
... Cell Ranger is not a "simple solution" in the sense that it requires large amounts of RAM, large amounts of temporary disk, and takes a very long time to process standard datasets. For example, in benchmarks we performed recently (https://www.biorxiv.org/content/10.1101/673285v2) we found that on th ...
written 14 months ago by Lior Pachter540
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Answer: A: about the use of CellRanger aggr
... You should not process the FASTQs together, because cell barcodes will clash. So you should process them separately. I would not recommend merging the replicates after processing, information about variance within condition will be useful and important for downstream analysis. If you do aggregate th ...
written 15 months ago by Lior Pachter540
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Comment: C: rnaseqcomp for own data withoutref genes
... RSEM is a widely used tool that produces good results by various benchmarks. On the other hand, a comparison between kallisto and Salmon is pointless because they have been shown in multiple comparisons to produce near identical results. For a recent reference for both these points see https://www.b ...
written 15 months ago by Lior Pachter540
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Comment: C: RNA-Seq: Getting Started with Kallisto
... Scripts for performing the gene-level differential analysis from the paper you cited are here: https://github.com/pachterlab/aggregationDE You should be fine with the annotated reference transcriptome as there is no need for a genome for this to work. ...
written 15 months ago by Lior Pachter540
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Answer: A: Build a Kallisto transcriptome index
... It sounds like your goal is to build an index from both the human and the Cassava Brown Steak Virus at the same time. You can do this by obtaining the transcriptomes for each separately, and then building an index using both files: `kallisto index -i name.idx human.fa.gz cassava_brown_steak_virus.f ...
written 15 months ago by Lior Pachter540
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Comment: C: Will Kallisto or Salmon perform streaming alignment from the Sequence Read Archi
... There is a blogpost describing how to do this for single-cell RNA-seq here: https://sinabooeshaghi.com/2019/07/09/fasterq-to-count-matrices-for-single-cell-rna-seq/ ...
written 15 months ago by Lior Pachter540
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Answer: A: RNA-Seq: Getting Started with Kallisto
... See https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth for a useful Snakemake workflow. ...
written 15 months ago by Lior Pachter540
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Answer: A: Dealing with 1000's of demultiplexed fastq files
... The [kallisto | bustools workflow][1] will allow you to specify the barcode / UMI /cDNA read structure and should be helpful for your analysis. [1]: https://www.kallistobus.tools/ ...
written 16 months ago by Lior Pachter540

Latest awards to Lior Pachter

Scholar 13 months ago, created an answer that has been accepted. For A: about the use of CellRanger aggr
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: about the use of CellRanger aggr
Scholar 13 months ago, created an answer that has been accepted. For A: about the use of CellRanger aggr
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: about the use of CellRanger aggr
Scholar 15 months ago, created an answer that has been accepted. For A: about the use of CellRanger aggr
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: about the use of CellRanger aggr
Pundit 4.3 years ago, created a comment with more than 10 votes. For C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
Commentator 5.1 years ago, created a comment with at least 3 up-votes. For C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.

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