User: 934963534

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93496353410
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Posts by 934963534

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Comment: C: How to simply extract certain filed from sam file
... sorry to bother again but I wonder if there is a way to speed up this process since my sam file is 140G and it is running really slowly... ...
written 12 weeks ago by 93496353410
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Comment: C: How to simply extract certain filed from sam file
... It works! Thanks a lot. ...
written 12 weeks ago by 93496353410
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How to simply extract certain filed from sam file
... Hello everyone. I have a sam file and only want to keep the read name and the FLAG field. How can I make it with awk?(And I do not want to keep the header) Thanks for your answer! ...
assembly samtools sam written 12 weeks ago by 93496353410 • updated 12 weeks ago by swbarnes23.8k
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How to use pacbio reads to join contigs
... Hello everyone! I have some pre-assembled contigs and want to join and extend the contigs using pacbio reads. I tried DBG2OLC on the contigs but the result shows that the contigs are even shorter. Does anybody know reasons or are there any other tools to join contigs with pacbio reads? Thanks for ...
tgs assembly long pacbio written 3 months ago by 93496353410 • updated 3 months ago by h.mon16k
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Comment: C: The --contig option for SPAdes
... I have read it before and wonder how the contigs help with graph construction, gap closure and repeat resolution, since they should not be considered just as single read. ...
written 3 months ago by 93496353410
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The --contig option for SPAdes
... Hello everyone, I am using the SPAdes with `--trusted-contigs` and `--untrusted-contigs`. I want to know how these contigs exactly help with graph construction and path extension. Is any document mentioned the related algorithms? ...
assembly contig spades written 3 months ago by 93496353410 • updated 3 months ago by dark.lord0
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Pacbio Metagenome alignment
... Can I use bwa to align metagenome pacbio reads to several reference genome? Or are there any other tools to achieve metagenome alignment for pacbio reads? ...
sequence alignment written 3 months ago by 93496353410 • updated 23 days ago by drkennetz310
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Comment: C: The reads simluted with wgsim
... So the first file may have the original orientation and the reverse orientation? ...
written 3 months ago by 93496353410
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The reads simluted with wgsim
... I am using wgsim to simulate reads from reference genome and I have a question. Is is always that the first output .fq file contians reads that has the same orientation as reference and the second contains the reverse complement orientation? ...
illumina next-gen wgsim sequencing written 4 months ago by 93496353410 • updated 4 months ago by Istvan Albert ♦♦ 77k
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Comment: C: The orientation of short reads on building de-Bruijn Graph
... So that's to say when traversing the graph, a node actually represents four conditions(forward(ACCT), backward(TCCA), forward-reverse(TGGA), backward-reverse(AGGT))? Would it cause more branches? ...
written 4 months ago by 93496353410

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