User: David

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David180
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Posts by David

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Comment: C: Assembly plasmid with tandem repeats of the same insert
... Sorry i meant aligning the repeat (25nt) to the assembled genome and visualize the plot , or extract coord with mummer to get the number of mapped repeats. Agree for aligning reads i would use minimap2. By the way the first run of flye did not work.” 0 disjointings assembled” although coverage, nu ...
written 4 weeks ago by David180
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Comment: C: Assembly plasmid with tandem repeats of the same insert
... Great Hugo !!! That´s exactly what i was following. Assembly reads with aligner (wtdbg2) but i will give flye a try. Then aligning reads with mummer to the reference. Really helpfull!!!! thanks ...
written 4 weeks ago by David180
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Assembly plasmid with tandem repeats of the same insert
... Hello, I got data from a lab , that is a plasmid that has been recently sequenced with nanopore. The plasmid is roughly 8kb and contains 40 copies of the same insert. I have the sequences of the plasmid and the insert. I would like to check that the plasmid does really contain the number of inserts ...
assembly sequencing written 4 weeks ago by David180 • updated 4 weeks ago by hugo.avila160
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Deseq2 with continous variable
... Hi, I would to see if there us any gene differentially expressed based on a continous variable (temperature) over age. I want to know exactly if there any genes that differ over age. I have the following design: > design(dds) = ~ Agegroup:temperature Agegroup has two factors: 20_40 and 41_70 ...
deseq2 written 5 months ago by David180 • updated 5 months ago by Kevin Blighe66k
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Comment: A: Remove fungi from human genome assemblies
... Yes i do have secondary aligments: samtools flagstat mapping.human.bam 141346 + 0 in total (QC-passed reads + QC-failed reads) 12798 + 0 secondary 44548 + 0 supplementary 0 + 0 duplicates 89377 + 0 mapped (63.23% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + ...
written 7 months ago by David180
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Comment: C: Remove fungi from human genome assemblies
... The -F 0x900 is for excluding secondary and supplementary alignments from the unmapped reads. I don´t see why secondary alignments would filter fungi unless human reads map to fungi ? ...
written 7 months ago by David180
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Comment: C: Remove fungi from human genome assemblies
... Yes that´s a metagenomics experiment on skin, i´m not interested in human , but bacteria and fungi. For some reasons fungi are filtered out: This is the command line: # Map ONT reads to human genome minimap2 -t10 -ax map-ont human_p38.3.fa ONT.reads.fq | samtools view --threads 10 -Sb ...
written 7 months ago by David180
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Comment: C: Remove fungi from human genome assemblies
... The fungi sequences are filtered together with the human genome, the reason why is because the human assemblies contain sequences that unfortunatly belong to contaminates (such as bacterial and fungi). These are hard to filter so was wondering. The following post from Brian bushnell (bbmap package ...
written 7 months ago by David180
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Remove fungi from human genome assemblies
... Hi, I´m mapping a set of ont long reads to the human genome: I´m using this genome version from gencode: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/GRCh38.p13.genome.fa.gz See description here: https://www.gencodegenes.org/human/ I´m using a skin sample so i expect to fin ...
dnaseq minimap written 7 months ago by David180 • updated 5 months ago by Biostar ♦♦ 20
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Answer: A: mummer dot plot
... Hi Alex, Definetly you are right (thanks for the figure)!!!!! Let me add more info to the discussion. The two genomes have been assembled from the same input pacbio dataset (RSII). The only difference is that one was assembled 3 years ago and the other yesterday with Flye. WOuld there be any expl ...
written 13 months ago by David180

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