User: julien.fouret.fr

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Posts by julien.fouret.fr

<prev • 10 results • page 1 of 1 • next >
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Comment: C: QUAST ignoring bam files
... I have always used QUAST but without bam Nothing is wrong about your bam and if you're using anaconda it should be also fine about dependencies... Maybe you could try to downgrade your QUAST version, it should be easy with anaconda: $ conda search quast Loading channels: done # Name ...
written 9 months ago by julien.fouret.fr20
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Comment: C: Analysing BAM files
... Yes. In my point of view, If this 5 varieties are very similar, the simpliest would be to avoid multiple alignment. ...
written 9 months ago by julien.fouret.fr20
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Comment: C: QUAST ignoring bam files
... What is the output of samtools flagstat ? Do you have the possibility to test the same command line using a container like https://hub.docker.com/r/staphb/quast/ ? Are the sequence IDs of your assemblies still matching what is present in your bam header ? ...
written 9 months ago by julien.fouret.fr20
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Comment: C: QUAST ignoring bam files
... Are you bam files indexed ( with samtools index ) ? ...
written 9 months ago by julien.fouret.fr20
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Comment: C: How to extract features from protein sequence for classification
... If you only have protein sequences, you'll need to first perform a blast against swissprot database. Then, you take the best hit and fetch the uniprot id (id mapping tools from uniprot). To match coordinates of your protein with the one linked with the uniprot id the best is to perform an global pai ...
written 9 months ago by julien.fouret.fr20
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Answer: A: How to extract features from protein sequence for classification
... You can fetch the following URL : "https://www.uniprot.org/uniprot/"+canonicalUniprotID+".txt" For example, let's consider the IFIT2 human; the uniprot id is P09913 You'll need to fetch : https://www.uniprot.org/uniprot/P09913.txt Of note, the lines you are interested in starts with "FT" Be ...
written 9 months ago by julien.fouret.fr20
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Answer: A: Analysing BAM files
... Hi, If you want the coordinates for the "same" region across the references, you can perform a genomic multiple alignment. You could use this tool : https://www.biorxiv.org/content/10.1101/730531v1 To be sure of the context what are your 5 references from ? Different species ? To avoid multi-ali ...
written 9 months ago by julien.fouret.fr20
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Answer: A: Finding of essential genes using database
... Hi, Are you using this link : http://tubic.org/deg_bak/ ? It seems that this database has moved here : http://www.essentialgene.org/ The following message appears on their website, > The new release is still under test. The old version is at: > http://tubic.org/deg_bak/ The Genome-BLAST s ...
written 9 months ago by julien.fouret.fr20
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Answer: A: Finding out gi number (Gene accession) from KO (KEGG orthology) numbers
... Hi, I think this might help you : https://www.uniprot.org/uploadlists/ Good luck ...
written 9 months ago by julien.fouret.fr20
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(Closed) mysql through proxy
... Hi Does anyone know how to use mysql through a proxy to contact ucsc db : jfouret@illumina-03:~$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A ERROR 2003 (HY000): Can't connect to MySQL server on 'genome-mysql.cse.ucsc.edu' (110) my proxy adress is `proxy.univ-lyon1.fr:3128` Th ...
software error written 4.6 years ago by julien.fouret.fr20 • updated 24 months ago by RamRS30k

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