Song Weichen

Hi Enformer developer, thanks for the great tool! I notice that the output of Enformer is the difference caused by a variant on the 5313 tracks. According to the nat...

Hi, I tried to run seqweaver on .fa input with the following Selene yml: >ops: [analyze] >model: { path: /lustre/home/acct-bmelgn/bmelgn-3/deepsea/models/seqweaver/seqweaver.py, class: Seqweaver, class_args: { n_classes: 217 } } analyze_sequences: !obj:selene_sdk.predict.AnalyzeSequences...

bcftools consensus error: No such sample

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Hi, I'm running consensus with the following code: `bcftools consensus -f int.fa -H 1 -s H1 haplotype.vcf.gz > id1.fa` The input haplotype.vcf is like > ##fileformat=VCFv4.2 #CHROM POS ID REF...

Dear Dan Thank you for your excellent tool. I'm analyzing WGS data for a trio and wish to get the de novo SVs. I ran sv2 separately for each person...

orderCells() returns "Quick-TRANSfer stage steps exceeded maximum"

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Hi monocle developer, i'm running monocle on large dataset(~40000*20000) on server, and i got message > Warning message: Quick-TRANSfer stage steps exceeded maximum (= 2008950) I found that estimateSizeFactors(),setOrderingFilter()&reduceDimension() had...

Could expecto accepts fasta input and return the prdicted tissue-specific expression values?

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Hi, thanks for the great tool! I notice that expecto takes a sequence around TSS to predict the tissue-specific expression values and calculate the expression difference between ref and alt...

Sorted file and dups/no dups files do not add up in dedup step

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Hi, thanks for the great tool! i'm running juicer on a pair of hic fastq and everything went well until the dedup step > scripts/juicer.sh -t 4 -S dedup -p...

Does reverse complement matter when using DNA sequence as input?

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Hi, i'm wondering if it is neccessary to reverse all input DNA sequence to positive strand when using sei. Biologically speaking both strand should have the same peak but i'm...

hicup deduplicator error in read.table function

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Hi, thanks for the great tool! i'm running hicup on one pair of fastq input, and all pipelines go well until deduplicator step: all intermediate files until .filt.bam were generated...

Hi, I notice that BASIL is a framework for large-scale LASSO of any distribution, and could be applied to continuous variables. So aside from snpnet which is designed for genotype...