User: lishen0709

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lishen07090
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Posts by lishen0709

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Comment: C: Finding Variable Genes in Seurat, scRNA-seq
... Hi igor. I am now facing the same problem. I don't know how to select correct parameters for x.low.cutoff, x.high.cutoff and y.cutoff. I also found that a little change in one of these parameters will lead to huge change in numbers of variable genes. I can get the plot as tutorial shows. But I don ...
written 4 weeks ago by lishen07090
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Comment: C: Is there something wrong with my Indel Calling protocol?
... All the pvalues of the ALT are 0.98. I once tried to change pvalue to 0.01. No ALT was detected under that situation. ...
written 5 weeks ago by lishen07090
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Is there something wrong with my Indel Calling protocol?
... hello everyone, I'm using BWA+SAMtools+Varscan to call indels to check my sgRNA cutting efficiency. The protocol I used is shown below: **1> set index:** bwa index hg38.fa **2> BWA-mem:** bwa mem -M hg38.fa XD01_R1.fastq XD02_R2.fastq > XD01.sam **3> sam 2 bam:** samtools view -bS X ...
indel genome alignment bwa rna-seq written 5 weeks ago by lishen07090
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How to deal with Segmentation fault in BWA?
... Hello everyone: I'm now using BWA to do alignment. But when I want to calculate the SA coordinate, It report an error: [sl2495@ruddle1 BWA_tool]$ bwa-0.7.17/bwa aln hg38.fa Project_Sc563/Sample_XD01/XD01_S1_L008_R1_001.fastq > XD01_S1_L008_R1_001.sai [bwa_aln] 17bp reads: max_diff = 2 [bwa_al ...
software error alignment rna-seq sequencing written 3 months ago by lishen07090 • updated 3 months ago by Pierre Lindenbaum104k

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