User: tans0307

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tans03070
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Posts by tans0307

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Problems with installation of Prodege decontamination software
... Dear @Brian, after analyzing my contigs using the ACDC software, I found out that the contigs of a sample that I had multiplexed with was present into my sample of interest. Do you have any suggestions on how I could go about tracing this source of contamination? Thanks! ...
written 3.1 years ago by tans03070
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Comment: C: Problems with installation of Prodege decontamination software
... Dear @Brian Bushnell, Do you have a literature that show that cross-library contamination is common with Illumina library-prep approaches? ...
written 3.1 years ago by tans03070
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Binning for multi-cell MDA samples
... Hello all, I have performed multi-cell FISH-FACS and downstream multiple displacement amplification. After decontamination of contigs, I have discovered the presence of two genomes. Most binning software were designed for normal metagenomics dataset, and not for multi-cell MDA. Will appreciat ...
genome next-gen written 3.2 years ago by tans03070
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Comment: C: Problems with installation of Prodege decontamination software
... Will take note of that, @genomax2 ...
written 3.2 years ago by tans03070
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Comment: A: Problems with installation of Prodege decontamination software
... Hello @Brian, I will like to clarify a few things. The synthetic artefacts were produced from an MDA amplification performed on sterile PBS (no genomic templates). Using the RiboTagger software (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1378-x), no RiboTags were observ ...
written 3.2 years ago by tans03070
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Comment: A: Problems with installation of Prodege decontamination software
... Dear @Brian, sorry for the tardy response. 1.) The sequencing was performed using an Illumina Hi Seq 2500 2.) The organism is a bacteria that is unclassified at the genus level 3.) The library was multiplexed with others 4.) I am not sure about this because the sequencing was performed by someo ...
written 3.2 years ago by tans03070
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Comment: C: Problems with installation of Prodege decontamination software
... @Brian, Thanks for your reply. I have generated contigs from an MDA-ed sample that was enriched via cell sorting. However, in my negative controls (no template), I have noticed the presence of artefact sequences. As such, I will like to remove these artefact sequences through binning. Prodege tool ...
written 3.2 years ago by tans03070
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Comment: C: Problems with installation of Prodege decontamination software
... @genomax2, these are the requirements for the installation of Prodege: - Blast+ 2.2.28 - Perl 5.16.0 (with modules Bio::SeqIO and Bio::Perl) - Prodigal 2.50 - R 3.0.1 The BLASTN_EXE envirnonmental variable is used to run blastn, R_EXE to run R, and PRODIGAL_EXE to run prodigal. Else, please use 'mo ...
written 3.2 years ago by tans03070
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Comment: C: Problems with installation of Prodege decontamination software
... @genomax2, thanks for your reply. Just to clarify things: 1.) I do not have to run the sh prodege_install.sh anymore? 2.) How do I define the correct locations? Which blastn: /home/tanshiming/tools/ncbi-blast-2.2.28+/bin/blastn Which R: /usr/bin/R Many thanks for your patience in this. :) ...
written 3.2 years ago by tans03070
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Problems with installation of Prodege decontamination software
... Hello people, I have tried downloading the stand-alone version of Prodege but I am having some issues. Untarring database files nt_euks.00.nhr nt_euks.00.nin nt_euks.00.nsq nt_euks.01.nhr nt_euks.01.nin nt_euks.01.nsq nt_euks.02.nhr nt_euks.02.nin nt_euks.02 ...
genome next-gen sequence blast sequencing written 3.2 years ago by tans03070 • updated 3.2 years ago by Biostar ♦♦ 20

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