User: johnnytam100

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johnnytam10040
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Posts by johnnytam100

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Is there any database that correlates annotation of a set of genes or gene ontology with the upstream regulatory genes (e.g. transcription factor)?
... Is there any database that correlates annotation of a set of genes or gene ontology with the upstream regulatory genes (e.g. transcription factor)? Thanks! ...
gene regulatory netwrok written 8 months ago by johnnytam10040 • updated 8 months ago by Jean-Karim Heriche16k
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samtools sort failed to merge tmp .bam file
... I tried to sort a .bam file with the following command /data/tam/script/bwa.kit/samtools sort libTTNRgenomemaster_map_lotusgenome.bam > libTTNRgenomemaster_map_lotusgenome.sorted.bam The following error, together with many ...bam.tmp.XXXX.bam files were generated (XXXX up to 1491) [ba ...
bam samtools bwa written 9 months ago by johnnytam10040
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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 10 months ago by johnnytam10040
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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 10 months ago by johnnytam10040
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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 10 months ago by johnnytam10040
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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 10 months ago by johnnytam10040
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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 11 months ago by johnnytam10040 • updated 11 months ago by 5heikki7.6k
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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 11 months ago by johnnytam10040
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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 11 months ago by johnnytam10040 • updated 11 months ago by Selenocysteine500
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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 11 months ago by johnnytam10040

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