rjg2186

BWA aln runs slower for first time and subsequent runs are faster

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Hi @lh3 , @bwlang , @jmarshall , @rmzelle , @sjackman I am executing BWA aln in google cloud VM and the first run for the day or first run after...

Issue with fastqc.smk

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Hi @Hoohm I am using the dropSeqPipe v0.4 and have installed snakemake using conda on custom directory. When I execute the pipeline, I am getting below error with fastqc.smk. Can...

Hi @Hoohm I am trying to run the pipeline using reads obtained from 1:1 mixture of human and mouse cell. How does the ratio in yaml needs to be justified...

Hi @brentp , @jashapiro , @nachocab , @wac , @lindenb Recently, I have been using bedtools fastaFromBed on hg38 fasta with index file to extract around 15000 sequences based on...

Using error corrected long reads

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Hi @adigenova , We just started using wengan for our assembly. Based on the documentation, I can understand it used raw pacbio or nanpore long reads. Could you please let...

Hi @JonathanShor , I have the UMI count matrix (genes by barcodes) from a mixed species experiments. The same barcode might also have few UMI counts in both human and...

Hi @swolock , I have a experiment with mixed human and mouse (equal proportion) scRNA-seq. Based on guideline from 10x, the I have provided the expected_doublet_rate as 6.4% expected_doublet_rate=0.064 I...