User: xunshengbu

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xunshengbu0
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Posts by xunshengbu

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Comment: A: Nanopore SNP and indels calling tool
... SNPs calling requires very high depth from reads with high quality, which both are challenges to Nano. Now it's possible to get high coverage NanoPore data, but not sure if anyone has estimated what's the minimum depth for NanoPore reads to call SNPs. ...
written 5 months ago by xunshengbu0
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Answer: A: Using SSPACE: Process 'extend/format contigs' failed when using -x extension opt
... Same issue here. SSPACE_Standard_v3.0.pl -l libraries.txt -s genome.scf.fasta -x 1 -T 36 -b sspace1 >& log_sspace1.txt & > Required inputs: > -l = libraries.txt > Number of paired files = 24 > -s = genome.scf.fasta > -b = sspac ...
written 12 months ago by xunshengbu0
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Answer: A: having trouble for running abyss-sealer as stand-alone application
... There should be a program abyss-sealer in the abyss-2.0.2/Sealer folder. You can move it to your abyss/bin. ...
written 2.1 years ago by xunshengbu0
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Comment: C: Nextseq for analysts
... Hi, Joe, quick question: have you notice the fastq files generated from bcl2fastq 2.17 have differences from the one generated by the basespace? I found some sequences has NNNNNs instead of sequences for 0.07% of the reads.   BTW, the bcl2fastq2 has an option --no-lane-splitting to merge fastq fil ...
written 3.7 years ago by xunshengbu0

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