User: 934963534

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93496353410
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Posts by 934963534

<prev • 16 results • page 1 of 2 • next >
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Comment: C: How to simply extract certain filed from sam file
... It works! Thanks a lot. ...
written 35 minutes 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 9 hours ago by 93496353410 • updated 9 hours ago by swbarnes23.4k
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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 9 days ago by 93496353410 • updated 9 days ago by h.mon13k
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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 10 days 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 11 days ago by 93496353410 • updated 7 days 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 4 weeks ago by 93496353410
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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 4 weeks 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 5 weeks ago by 93496353410 • updated 5 weeks ago by Istvan Albert ♦♦ 76k
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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 5 weeks ago by 93496353410
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The orientation of short reads on building de-Bruijn Graph
... I know a node can refer to the orignal kmer and its forward-reverse kmer, but how to deal with the problem that these short reads can also be in different orientation to the reference. For example, given genome reference AAACCT, should ACCT(TGGA)(forward) and TCCA(AGGT)(backward) considered also a s ...
assembly sequence de-bruijn graph written 5 weeks ago by 93496353410 • updated 5 weeks ago by Devon Ryan78k

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