User: kanshenglong

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Posts by kanshenglong

<prev • 13 results • page 1 of 2 • next >
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How to run Velvet in multiple k-mers?
... Hello members, I would like to run velvet in multiple k-mers. The velveth run noamally($velveth /work_dict/ 31,35,2 -fastq.gz -shortPaired -separate reads_1.fastq.gz reads_2.fastq.gz), but when run velvetg there still wrong($velvetg /work_dict/ -cov_cutoff 5 -ins_length 250 -ins_length_sd 40 -ex ...
genome velvet multiple k-mers written 13 months ago by kanshenglong0
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Comment: C: extract nanopore reads from the bam/sam file
... Thanks for your help!! ...
written 23 months ago by kanshenglong0
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Comment: C: extract nanopore reads from the bam/sam file
... Thanks for your useful answer. And would you like to teach me to gather the headers of the mapped reads and retrieve the full reads from original data file. ...
written 23 months ago by kanshenglong0
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Comment: C: extract nanopore reads from the bam/sam file
... What puzzles me is the command of filtering illumina reads same as nanopore reads? Thanks! ...
written 23 months ago by kanshenglong0
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Comment: C: extract nanopore reads from the bam/sam file
... Yes. I did this mapping by myself. And I am looking forward to get only mapped/unmapped reads. I mean to filter the nanopore reads which is identity with plastid genome by graphmap and samtools. So I can prevent from nuclear contamination when I assemble plastid genome. Thanks for your help! ...
written 23 months ago by kanshenglong0
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extract nanopore reads from the bam/sam file
... Hi, After mapping the nanopore reads on the reference Genome, I want to extract raw reads from the bam/sam file. Can someone help me here? Thank you in advance!! ...
genome alignment next-gen written 23 months ago by kanshenglong0
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Comment: C: How to construct multiple sequence alignment from group of pairwise alignments
... jrj.healey: Thanks for your reply! I'm sorry I did not make it clear. As my sequences are much longer than the reference sequence, I can't align these sequences by Multiple Sequence Alignment. I want this result. ![enter image description here][1] result [1]: https://s24.postimg.org/6u9 ...
written 3.7 years ago by kanshenglong0
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Comment: A: How to construct multiple sequence alignment from group of pairwise alignments
... Someone has asked this question, But I can't run this script. http://www.perlmonks.org/bare/?node_id=866127 Thank you !! ...
written 3.7 years ago by kanshenglong0
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How to construct multiple sequence alignment from group of pairwise alignments
... I have a bunch of 10 or more very closely related DNA sequences (from different strains) aligned to a reference chromosome. How can I generate multiple sequence alignment along with "reference" of all these sequences without affecting individual alignments to the reference. Don't cut the blank sequ ...
alignment written 3.7 years ago by kanshenglong0 • updated 3.7 years ago by genomax89k
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Comment: A: local alignment with a sets of sequences in a fasta file to a reference sequence
... Can I retrieve such alignment in a fasta format? Thanks a lot. ...
written 4.1 years ago by kanshenglong0

Latest awards to kanshenglong

Popular Question 12 months ago, created a question with more than 1,000 views. For pairwise alignment with multiple sequences in a fasta file.
Popular Question 22 months ago, created a question with more than 1,000 views. For local alignment with a sets of sequences in a fasta file to a reference sequence.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For pairwise alignment with multiple sequences in a fasta file.
Popular Question 3.7 years ago, created a question with more than 1,000 views. For pairwise alignment with multiple sequences in a fasta file to a reference sequence.

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