User: bas1993

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bas199340
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Netherlands
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2 months ago
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1 year, 7 months ago
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b**********@hotmail.com

Posts by bas1993

<prev • 10 results • page 1 of 1 • next >
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Comment: A: analyse bam file
... Besides Bedtools and samtools, I think [Bamstats][1] is also useful. [1]: http://bamstats.sourceforge.net/ ...
written 3 months ago by bas199340
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Comment: C: How to extract genome files based on genome ID
... in the script that you showed above I think you need the line with eval. If you use the command line below you can see what "eval" does: help eval But for creating a blast database with all the fna files you don't really need a script as you could also just type out the two lines that you nee ...
written 3 months ago by bas199340
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Comment: C: How to extract genome files based on genome ID
... You can change the command line above with the full path. for i in $(cat list.txt); do mv fna/"$i".fna.bz2 fna/filtered/; done And if you need to uncompress your genome files also then you can use what Lieven Sterck wrote. ...
written 3 months ago by bas199340
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Should I upload my assemblies to NCBI Genbank, Genome or WGS?
... I have complete (every structure in 1 contig) and fragmented (every structure in multiple contigs) assemblies of bacteria that are part of 1 Bioproject/study. But I am not sure if I should upload these assemblies to NCBI genbank, Genome or WGS batch. Or should I upload all complete assemblies to ...
ncbi assembly written 3 months ago by bas199340
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Answer: A: How to extract genome files based on genome ID
... for i in $(cat list.txt); do mv "$i".fna.bz2 fna/filtered/; done Where list.txt is your list of high quality genomes and filtered/ is a new directory. ...
written 3 months ago by bas199340 • updated 3 months ago by lieven.sterck8.9k
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How to detect which plasmids occur multiple times in a collection of fragmented whole genome assemblies?
... I have whole genome assemblies of >100 bacterial isolates that are very fragmented (short read sequencing, MiSeq). In this dataset I determined that there are various plasmids present with PlasmidFinder. I want to do long read sequencing on a small selection within this collection, but I want to ...
plasmid next-gen blast alignment sequencing written 4 months ago by bas199340 • updated 4 months ago by hugo.avila160
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Comment: C: How to see how many times a sequence of ~7000 bp occurs in long reads?
... To give some more background information, I didn't knock in the gene myself but a whole plasmid is integrated in the chromosome by an external company in a food bacteria. The documentation of this modification is not correct and that is why we sequenced it. The plasmid is around 7000 basepairs and I ...
written 19 months ago by bas199340
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Comment: C: How to see how many times a sequence of ~7000 bp occurs in long reads?
... I already did an assembly and in the .gfa files it looked like circular contig that is connected to the chromosome. So I hypothised that maybe the assembly was influenced by some of the reads that are shorter than the modification. That is why I extracted all the reads that are longer than the modif ...
written 19 months ago by bas199340
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Comment: C: How to see how many times a sequence of ~7000 bp occurs in long reads?
... But will I not get the same problem as with other mappers. I know the genetic modification is present in the reads, but I would like to know if it is present multiple times (or 1 time completely and then half of the sequence). ...
written 19 months ago by bas199340
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How to see how many times a sequence of ~7000 bp occurs in long reads?
... So I have pacbio and MinION reads and I want to know if a genetically modified region is 1 time present or multiple times. Normal mapping doesn't give me the answers that I want as the reads are soft-clipped on the known sequence so I have no information about what else is in the read. So instead of ...
alignment next-gen sequencing written 19 months ago by bas199340 • updated 18 months ago by Biostar ♦♦ 20

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Scholar 3 months ago, created an answer that has been accepted. For A: How to extract genome files based on genome ID

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