User: shira.zaltsman

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Posts by shira.zaltsman

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Comment: C: GridION fastq ASSEMBLY
... look like Flye, didn't work for viruses. what tool is good for alignment? I need to get a sequence ...
written 8 weeks ago by shira.zaltsman20
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Comment: C: GridION fastq ASSEMBLY
... [1]: https://ibb.co/jLbYr48 ...
written 8 weeks ago by shira.zaltsman20 • updated 8 weeks ago by genomax84k
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Comment: C: GridION fastq ASSEMBLY
... I checked in BLAST to see if there is an overlap and there is ![enter image description here][1] [1]: https://ibb.co/jLbYr48 ...
written 8 weeks ago by shira.zaltsman20
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Comment: C: GridION fastq ASSEMBLY
... thanks! I installed Flye, but it yields an error: flye --nano-corr /data/tom/CORONA/fastq/SRR11313278.fastq.gz --genome-size 30k --min-overlap 1000 --out-dir /data/tom/CORONA/test [2020-04-05 17:26:26] INFO: Starting Flye 2.7-b1587 [2020-04-05 17:26:26] INFO: >>>STAGE: conf ...
written 8 weeks ago by shira.zaltsman20
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GridION fastq ASSEMBLY
... Hey friends! I have a large number of fastq files of COVID-19 from GridION sequencing, I want to produce FASTA files of the assembly results. because the size of the reads is large (about 800-1200 bases) TRINITY didn't work well for me. what other tools can I use to assembly these files?? BTW: I wa ...
assembly fastq nanopore written 8 weeks ago by shira.zaltsman20
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Comment: C: pathogenic bacteria in the SRA database
... thank you for your answer, but I am looking for a way to do this thing automatically by writing a bash script that would download for me full bacterias genome using SRA entries, and the input is just a bacteria full name. I need also to find a way to separate the genomes to a pathogen and not pathog ...
written 19 months ago by shira.zaltsman20
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pathogenic bacteria in the SRA database
... where it says that the sample is from pathogenic bacteria in the SRA database? for example, I want to download only SRA samples of a pathogenic Acinetobacter baumannii. is there some filter for that? ...
ncbi sra bacteria pathogen written 19 months ago by shira.zaltsman20 • updated 19 months ago by vkkodali2.0k
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Comment: A: primer3 parameter input
... please do not direct me to the manual. unless its specific subject there ...
written 21 months ago by shira.zaltsman20
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primer3 parameter input
... I have a few 50bp sequence of a bacteriaas genome, I am trying to find primers using primer3 on linux. this is my input (in file "example.txt"): SEQUENCE_ID=example SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGAC ...
gene bacteria help primer3 linux written 21 months ago by shira.zaltsman20 • updated 21 months ago by Pierre Lindenbaum128k
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Comment: A: Parsing Blast output on linux/unix
... I'm having the same problem :( ...
written 2.0 years ago by shira.zaltsman20

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For primer3 parameter input

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