User: johnnytam100

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johnnytam10020
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Posts by johnnytam100

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Comment: C: Suggestion on contig assembler which respect a single copy mutation in a nonaplo
... There is one [example][1] but is for a diploid relative species and I think there is no projects working on nonaploid of this species... Let me ask if I could do some long reads... More suggestions on wet or dry experiments would be much appreciated! [1]: https://www.ncbi.nlm.nih.gov/pubmed/ ...
written 21 days ago by johnnytam10020
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Comment: C: Suggestion on contig assembler which respect a single copy mutation in a nonaplo
... I used 150bp illumina library... coverage of wildtype is 11 and mutant is 38. Do you suggest getting some long reads anyway? ...
written 22 days ago by johnnytam10020
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Comment: C: Typical % of unmapped reads to genome contigs assembled from the same library?
... I used `samtools flagstat .bam` for mapping results of the contigs from SPades and gave me the following output : 10083388 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 1665199 + 0 mapped (16.51% : N/A) 0 + 0 paired in ...
written 23 days ago by johnnytam10020
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Typical % of unmapped reads to genome contigs assembled from the same library?
... I have an Illumina 150bp whole-genome library of a plant species (genome size ~7.5Gb), using the library I : 1) assembled genome contigs (using SPades, SOAP and platanus) and 2) map the same library to the contigs from 1) using bwa mem I discover, using `splitsam.sh` from [BBMap][1] to give me ...
assembly mapping bwa written 23 days ago by johnnytam10020
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Recommendation on k-mer counting package for multiple libraries?
... I want to count all the 30-mers (or partially e.g. every 30-mer starting with "A") in multiple libraries to produce a k-mer abundance table partly like this : kmer lib1 lib2 lib3 lib4 lib5 AAAAAAAAAAAAAAAAAAAAAAAAAGAGAA 0 0 2 6 4 AAAAAAAAAAAAAAAAAAAAAAAAAGATCT 0 1 1 0 2 AAAAAAAAAAAA ...
kmer written 27 days ago by johnnytam10020 • updated 27 days ago by 5heikki6.9k
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Comment: C: Platanus assembler : unable to start contig assembly, any problem with the comma
... Solved, actually it's the opposite, I delete the 2, which was originally present in the example given by the [manual][1] : Platanus assemble –o Pxut –f ./DRR02167[34]_[12].fastq –t 16 –m 128 2> assemble.log Thank you! [1]: http://platanus.bio.titech.ac.jp/?page_id=2 ...
written 28 days ago by johnnytam10020
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Platanus assembler : unable to start contig assembly, any problem with the command?
... I used the following command in hope to start the contig assembly using Platanus : /data/tam/script/platanus/platanus assemble -f /data/tam/genome/reads/kmer_containing_reads/TTN_3TTN_TTNR1_for_contig/step4_TTN_3TTN_TTNR1_master.fastq -o 1d_TTN_3TTN_TTNR1_for_contig_platanus -m 128 -t 16 2 > ...
platanus written 28 days ago by johnnytam10020 • updated 28 days ago by Selenocysteine330
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Comment: C: Sam FLAGS : how could a read be described as "read unmapped" but "read in revers
... Thank you very much! :) ...
written 4 weeks ago by johnnytam10020
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Suggestion on contig assembler which respect a single copy mutation in a nonaploid genome?
... As title, and the following is the background FYI : I am discovering a possible single copy insertional mutation in a nonaploid plant genome. Previously I used SPades to assemble contigs of the mutant using reads containing the potentially mutated sequence, which then has given me a ~1000 contigs ...
indel assembly insertion deletion written 4 weeks ago by johnnytam10020
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Comment: C: Choosing sam flags to extract all reads mapped to 5' -> 3' OR 3' -> 5' of refere
... So Splitsam will output forward.sam and reverse.sam. How about the `plus.sam` and `minus.sam`? Are they also input files? Thank you! ...
written 4 weeks ago by johnnytam10020

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