User: marongiu.luigi

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Posts by marongiu.luigi

<prev • 82 results • page 1 of 9 • next >
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Comment: C: create GFF file for fasta reference file
... this time worked fine. This exception then no longer stand. ...
written 4 days ago by marongiu.luigi120
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Comment: C: create GFF file for fasta reference file
... I am re-running. My esearch/efetch is version 7.00 ...
written 5 days ago by marongiu.luigi120
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Comment: C: create GFF file for fasta reference file
... OK, so it is not possible from a fasta file but it is possible from a GB file. Fair enough, thank you! For matter of completion, I could not produce a GB file for the taxon 10239: when i ran the command esearch -db "nucleotide" -query "txid10239[Organism] AND refseq[filter]"|efetch -format gb ...
written 5 days ago by marongiu.luigi120
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Comment: C: create GFF file for fasta reference file
... I have for instance all the viruses with esearch -db "nucleotide" -query "txid10239[Organism] AND refseq[filter]"|efetch -format fasta > virus_genome.fa ...
written 6 days ago by marongiu.luigi120
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create GFF file for fasta reference file
... hello, i am downloading the reference sequence for all the species within a given taxon with the command: esearch -db "nucleotide" -query "txidX[Organism] AND refseq[filter]"|efetch -format fasta > genome.fa this is supposed to be a chromosome to align my reading against. But how can I vis ...
genome sequence rna-seq written 6 days ago by marongiu.luigi120
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Comment: C: Get reference full genome sequences for selected organisms
... thank you, but the taxon I am looking for contains both complete genomes and sequences; still is there a way to separate them, either directly with an option of esearch or afterward with the manipulation of the resulting fasta file? ...
written 11 days ago by marongiu.luigi120
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Get reference full genome sequences for selected organisms
... Hello, I would like to download all the reference sequences, full length for a given organism. I am using esearch as reported on the [NCBIwebsitee][1] with the following command: esearch -db "nucleotide" -query "txidX[Organism] AND refseq[filter]"|efetch -format fasta > genome.fa where X i ...
genome blast written 12 days ago by marongiu.luigi120 • updated 12 days ago by Joseph Hughes2.4k
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Comment: C: BLAT installation *** No rule to make target '../lib//jkweb.a', needed by 'blat'
... Thank you, the link seems very good. This time i ran: $ echo $MACHTYPE x86_64-pc-linux-gnu $ MACHTYPE=x86_64 $ export MACHTYPE $ echo $MACHTYPE x86_64 $ export PATH=~/bin/x86_64::$PATH $ make and the following files are created in ~/bin/x86_64/ $ ls blat ...
written 21 days ago by marongiu.luigi120
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Comment: A: BLAT installation *** No rule to make target '../lib//jkweb.a', needed by 'blat'
... I use `sudo` because of the privileged location /usr/... when building without privileges I sometimes got problems with writing permissions. anyhow even with `make` only I got the same error. ...
written 21 days ago by marongiu.luigi120
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BLAT installation *** No rule to make target '../lib//jkweb.a', needed by 'blat'
... Dear all, I am trying to install BLAT. As specified in the README file that accompanies the package I created the folder ~/bin/$MACHTYPE. My MACHTYPE variable is > x86_64-pc-linux-gnu which matches with the directory blatSrc/lib/x86_64 contained in BLAT. I added ~/bin/x86_64-pc-linux-gnu to ...
software error assembly written 21 days ago by marongiu.luigi120

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