User: Thomas B.

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Thomas B.10
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Posts by Thomas B.

<prev • 9 results • page 1 of 1 • next >
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How to perform PCA on gene expression?
... Hi, I am interested in the identification of marker genes of infection by a parasite. I have several biological samples corresponding to different infection stages. I quantified the expression of genes that are though to be differentially expressed by qPCR. Now I would like to run a principal comp ...
marker gene gene expression pca qpcr clustering written 6 weeks ago by Thomas B.10 • updated 6 weeks ago by ahmad mousavi340
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Answer: A: Memsat-SVM: error running PSI-BLAST
... I added the following lines to my .ncbirc file and it solved the problem. [BLAST] BLASTDB=/home/thomas/Softwares/memsat-svm/database/uniprot_sprot.fasta ...
written 11 weeks ago by Thomas B.10 • updated 11 weeks ago by RamRS19k
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Memsat-SVM: error running PSI-BLAST
... Hi, I try to install Memsat-SVM on my computer but face an issue that I am not able to fix. Here is what I did: > - Compile Memsat-svm > > `tar -zxvf memsat-svm1.3.tar.gz` > > `cd memsat-svm` > > `make` > > - Build database > > `mkdir databa ...
software error memsat-svm psi-blast written 12 weeks ago by Thomas B.10
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Comment: C: How to extend BAC sequences with Pacbio reads in order to rebuild a genomic regi
... The BACs were individually assembled using HGAP. Each output sequence was checked considering read alignment (BAM file), size (fingerprinting), and BAC ends (Sanger). I cannot exclude some errors but I am confident in this dataset. You are right, scaffolding is maybe a good option and I'll look i ...
written 13 months ago by Thomas B.10
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Comment: C: How to recompute coding sequences from a psl format ?
... Oh wait, there is a nice `--exons=genomic` option in GMAP that does what I want. However the output should be processed (something like `cat my_report.txt | grep -v '<' > my_report.fasta`) in order to obtain a true FASTA file. It seems also that if there are multiple matches for a same query, ...
written 13 months ago by Thomas B.10
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Comment: C: How to extend BAC sequences with Pacbio reads in order to rebuild a genomic regi
... The whole genome size is estimated at 770Mb. The raw dataset is ~5.8M reads (coverage ~75x) and the error-corrected/trimmed dataset is ~1.4M reads (coverage ~20x). We did assemble the whole genome using Canu and Falcon, but there exist structural mis-assemblies in both cases (not able to align BAC ...
written 13 months ago by Thomas B.10
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Comment: C: How to recompute coding sequences from a psl format ?
... Hi Kevin, Thanks for your reply! I converted my PSL file to BED using psl2bed as you suggested. psl2bed < my_report.psl > my_report.bed I then used the online bed_to_gff_converter tool from Galaxy to convert the BED file to GFF. I finally used gffread to extract FASTA sequences as you a ...
written 14 months ago by Thomas B.10
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How to extend BAC sequences with Pacbio reads in order to rebuild a genomic region?
... Hi all, I am focusing on the reconstruction of a ~2Mb plant genomic region. What I have is some BAC sequences from there and Pacbio reads from the whole genome. I am interested in extending the non-overlapping BAC sequences with Pacbio reads up to be able to merge them and obtain a unique referen ...
assembly tadpole written 14 months ago by Thomas B.10
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How to recompute coding sequences from a psl format ?
... Hi everyone, I mapped coding sequences (CDSs) onto a genome using GMAP and got a report in psl format. Is there a readily available tool / way to extract the genome sequences that matched - I mean those that correspond to blocks - then recompute coding sequences ? ...
genome alignment sequence gmap cds written 14 months ago by Thomas B.10 • updated 6 months ago by Biostar ♦♦ 20

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