User: shelkmike
shelkmike • 310
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Mikhail Schelkunov
Posts by shelkmike
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... I recommend to use [fastp](https://github.com/OpenGene/fastp). It is able to automatically guess adapter sequences in your reads and trim them, you don't even have have to know which adapters are in your reads. ...
written 1 day ago by
shelkmike • 310
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... 1) Imagine that you sequenced some plant and deposited its genome in GenBank without removing contamination. Then, all the bacterial sequences that you deposited will be indicated in GenBank as plant sequences. This will highly decrease the precision of taxonomic classification for future scientists ...
written 10 days ago by
shelkmike • 310
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Comment:
C: combine trinity outputs
... Did you try to run Trinity with in silico normalization to 50x coverage using all reads? I think, this would be the best solution if you don't have enough RAM. ...
written 19 days ago by
shelkmike • 310
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... You may want to look at the "Extraction of UMI reference sequences" paragraph in the paper "Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing" (https://www.biorxiv.org/content/10.1101/645903v3.full ). Authors had a similar task ...
written 20 days ago by
shelkmike • 310
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... I usually do the following:
1) Align all contigs by BLASTN to the NCBI NT database.
2) Using the NCBI Taxonomy database determine taxonomies of best matches.
3) Remove contigs whose best matches were from improper taxons. If you assemble a genome of a plant belonging to Embryophyta, you may want to ...
written 22 days ago by
shelkmike • 310
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C: MiSeq 2*250 read length
... What do you mean by "1002 read length"? ...
written 22 days ago by
shelkmike • 310
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... Not related to RAM consumption, but you run Spades in a wrong way. If you have three libraries, you should provide them with --pe1-1, --pe1-2, --pe2-1, --pe2-2, --pe3-1, --pe3-2. The number after "pe" is the number of the library. ...
written 24 days ago by
shelkmike • 310
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... Spades monitors RAM usage during its run. Can you look into its logs and find what was the RAM usage before Spades crashed?
Another method to find peak RAM consumption of a program is to run it with a command which starts from "/usr/bin/time -v", in your case the command will be:
/usr/bin/time ...
written 24 days ago by
shelkmike • 310
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... There are many ways to do this. I suggest to do the following:
1) Align your genome to the reference genome using pairwise [megablast](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=MegaBlast&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&DATABA ...
written 24 days ago by
shelkmike • 310
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... This is normal for reads with very high quality. Such high quality is not frequently achieved, so I congratulate you :) ...
written 4 weeks ago by
shelkmike • 310
Latest awards to shelkmike
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For A: Criteria for filtering contigs after spades assembly
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created an answer with at least 3 up-votes.
For A: How to extend contigs from single-end reads?
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12 months ago,
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For Phylogeny from incomplete orthogroups
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For A: Criteria for filtering contigs after spades assembly
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For Is BUSCO really better than CEGMA for genome assembly quality evaluation?
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2.9 years ago,
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