User: doinelpierrot

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Posts by doinelpierrot

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Quality Check of Samples and Biological Replicates
... Ok thanks for your answers so I have a new PCA plot with all the names of samples (and the batch number after the "B" ![PCA][1] I have plot expression (kallisto raw count) B2_1 vs B1_12 ![B2_1 vs B1_12][2] and B4_3 vs B4_1 ![B4_3 vs B4_1][3] In the both cases the variance seems to be partially exp ...
written 22 days ago by doinelpierrot10
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Comment: C: Quality Check of Samples and Biological Replicates
... Ok thanks for your answer so I have a new PCA plot with all the names of samples (and the batch number after the "B" ![PCA][1] I have plot expression (kallisto raw count) B2_1 vs B1_12 ![B2_1 vs B1_12][2] and B4_3 vs B4_1 ![B4_3 vs B4_1][3] In the both cases the variance seems to be partially expl ...
written 22 days ago by doinelpierrot10
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Comment: C: Quality Check of Samples and Biological Replicates
... Thanks for your answer ! What would be your axes for the X-Y plots ? ...
written 24 days ago by doinelpierrot10
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Comment: C: Quality Check of Samples and Biological Replicates
... I have no obvious explanation that could explain this apart from randomness or the fact that the change of temperature has little impact on the transcriptional response, or handling mistakes ... So I am wondering now if it is relevant and worth the effort to pursue a long analysis of differentially ...
written 24 days ago by doinelpierrot10
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Quality Check of Samples and Biological Replicates
... Hello, I am performing differential gene expression analysis between to condition of temperature (A and B). I have the matrix of count for all my genes and the 5 replicates for each condition. When I perform a PCA following the [Deseq2 biocondutor guide][1], my replicates seems not so well [correl ...
R rna-seq assembly written 27 days ago by doinelpierrot10
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Getting Uniprot accession number
... Hello, I have a table full of Uniprot protein names and an uniprot identifier like this : ANTR6_ARATH. https://www.uniprot.org/uniprot/Q3E9A0&format=html It is supposed to be the gene id, however when I use https://biodbnet-abcc.ncifcrf.gov/db/db2db.php with ANTR6_ARATH as a gene id input I ha ...
gene rna-seq written 4 weeks ago by doinelpierrot10
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Comment: A: Blast command line
... I have tried sallacc and it gives me also the swissprot accession. Is there any way to also get the ncbi accession (for instance O75925 for PIAS1_HUMAN) ? ...
written 7 weeks ago by doinelpierrot10
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Blast command line
... Hello all, * I would like to run a blastx on a fasta file in order to perform a quick functionnal annotation on swissprot. * So I ran succesfully : blastx -query "${QUERY}" -db "${BANK}" -out ${OUT_FILE} -max_target_seqs 1 ${BLAST_PARAM} -num_threads $NCPUS -outfmt "6 qseqid sseqid sacc p ...
software error sequence rna-seq written 7 weeks ago by doinelpierrot10
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Comment: C: Is it possible to estimate the proportion of contamination from GC contents ?
... I have thougt about it but I can't blast 200 Gb of reads, I reduce considerably the data after assembly. Besides it seems to be a multi species contamination and I don't have the full genomes/transcriptomes of these associated species. So the other alternativethat was to identify the contaminants fr ...
written 11 weeks ago by doinelpierrot10
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Comment: C: Is it possible to estimate the proportion of contamination from GC contents ?
... I am doing de novo assembly. So far I am thinking of doing a pre-assembly with my samples with good gc content and then blast all my transcript to delete stranger transcripts. And then mapping all my reads to this transcriptom. And eventually do a final assembly with all mapping reads. ...
written 11 weeks ago by doinelpierrot10

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