User: shelkmike

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shelkmike310
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Mikhail Schelkunov

Posts by shelkmike

<prev • 47 results • page 1 of 5 • next >
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Answer: A: How to trim reads when I'm not sure where they are?
... 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 shelkmike310
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Comment: C: How can I remove contaminants from an assembled genome?
... 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 shelkmike310
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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 shelkmike310
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Answer: A: Alignment of short sequences allowing gaps and wildcards
... 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 shelkmike310
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Answer: A: How can I remove contaminants from an assembled genome?
... 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 shelkmike310
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Comment: C: MiSeq 2*250 read length
... What do you mean by "1002 read length"? ...
written 22 days ago by shelkmike310
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Comment: C: Error in malloc (SPAdes assembler)
... 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 shelkmike310
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Answer: A: Error in malloc (SPAdes assembler)
... 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 shelkmike310
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Answer: A: bacterial genome assembly output from canu
... 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 shelkmike310
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Answer: A: Fastq file with very high per base sequence quality and no box-whisker plot
... 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 shelkmike310

Latest awards to shelkmike

Scholar 4 months ago, created an answer that has been accepted. For A: Criteria for filtering contigs after spades assembly
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to extend contigs from single-end reads?
Voter 11 months ago, voted more than 100 times.
Popular Question 12 months ago, created a question with more than 1,000 views. For Phylogeny from incomplete orthogroups
Scholar 22 months ago, created an answer that has been accepted. For A: Criteria for filtering contigs after spades assembly
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Is BUSCO really better than CEGMA for genome assembly quality evaluation?
Scholar 2.9 years ago, created an answer that has been accepted. For A: Criteria for filtering contigs after spades assembly
Supporter 4.2 years ago, voted at least 25 times.

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