User: Lior Pachter

gravatar for Lior Pachter
Lior Pachter300
Reputation:
300
Status:
Trusted
Location:
United States
Website:
https://pachterlab.git...
Twitter:
@lpachter
Last seen:
6 hours ago
Joined:
3 years, 11 months ago
Email:
l*******@caltech.edu

Posts by Lior Pachter

<prev • 26 results • page 1 of 3 • next >
1
vote
0
answers
88
views
0
answers
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 2 days ago by Lior Pachter300
0
votes
3
answers
235
views
3
answers
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 5 days ago by Lior Pachter300
0
votes
1
answer
117
views
1
answers
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 7 days ago by Lior Pachter300
0
votes
1
answer
412
views
1
answers
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 9 days ago by Lior Pachter300
2
votes
3
answers
235
views
3
answers
Answer: A: RNA-Seq: Getting Started with Kallisto
... See https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth for a useful Snakemake workflow. ...
written 11 days ago by Lior Pachter300
2
votes
4
answers
367
views
4
answers
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 24 days ago by Lior Pachter300
1
vote
2
answers
414
views
2
answers
Answer: A: UMI Tools Dedup
... The [kallisto | bustools workflow][1] has a very low memory footprint. [1]: https://www.kallistobus.tools/ ...
written 24 days ago by Lior Pachter300
2
votes
0
answers
186
views
0
answers
Comment: C: Which bias flags to run with Salmon before DESeq2 analysis?
... It's helpful to look at how the authors of Salmon run Salmon. Sometimes they use `--seqBias --gcBias --posBias --validateMappings` (see [here](https://github.com/csoneson/annotation_problem_txabundance/blob/master/makefiles/Salmon.mk)) and sometimes they use only `--gcBias` (see [here](https://gith ...
written 25 days ago by Lior Pachter300 • updated 24 days ago by RamRS22k
0
votes
3
answers
389
views
3
answers
Answer: A: Hardware requirement for RNA-seq
... You are right that salmon is similar to kallisto, however kallisto is faster, a relevant matter if one is working on a Mac desktop. https://liorpachter.wordpress.com/2017/08/02/how-not-to-perform-a-differential-expression-analysis-or-science/ ...
written 4 months ago by Lior Pachter300
0
votes
1
answer
412
views
1
answers
Comment: C: Will Kallisto or Salmon perform streaming alignment from the Sequence Read Archi
... You can see an example of a snakemake script to do this with kallisto here: [https://github.com/pachterlab/bears_analyses] Not streaming but could be modified to do so. ...
written 10 months ago by Lior Pachter300

Latest awards to Lior Pachter

Pundit 3.0 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 3.9 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.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1880 users visited in the last hour