User: Sej Modha

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Sej Modha2.3k
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Glasgow, UK
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http://bioinformatics....
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SejModha
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Posts by Sej Modha

<prev • 348 results • page 1 of 35 • next >
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Comment: C: art_illumina use custom error profile to simulate reads
... Thanks @genomax! I've updated my previous comment. ...
written 11 hours ago by Sej Modha2.3k
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Comment: C: art_illumina use custom error profile to simulate reads
... Edited to include correct URL - Well, in that case, you might want to look into other tools such as BBMap - https://sourceforge.net/projects/bbmap/ ...
written 12 hours ago by Sej Modha2.3k
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Comment: A: art_illumina use custom error profile to simulate reads
... Have you tried using an older version of the software such as [ART-GreatSmokyMountains-04-17-2016][1] that has a built-in MiSeq profile? [1]: https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm ...
written 13 hours ago by Sej Modha2.3k
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Answer: C: biomaRt: Cannot access the zebra fish dataset
... This is reported on the [support forum of the bioconductor][1] by other users too. A workaround is also presented there: https://support.bioconductor.org/p/104025/ [1]: https://support.bioconductor.org/p/104025/ ...
written 15 hours ago by Sej Modha2.3k
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Comment: C: Adding Percentage in PCA
... Did you try 3.4 The percentage code from http://huboqiang.cn/2016/03/03/RscatterPlotPCA ...
written 1 day ago by Sej Modha2.3k
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Comment: C: issue with fasttree package
... I am unable to replicate the same error at my end with your data as the output file generated for me is in FASTA format. It is worth generating output file in the clustalw format and converting them using online tools such as https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/ ...
written 5 days ago by Sej Modha2.3k
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Comment: C: issue with fasttree package
... Input file you provided here is in FASTA (https://en.wikipedia.org/wiki/FASTA_format) format but contains only Ns in the sequences, the output file is not in the FASTA format. Are you sure you want to run FastTree on such data that only contain Ns? ...
written 6 days ago by Sej Modha2.3k
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Comment: C: issue with fasttree package
... What is the format of the MUSCLE alignment file? Is it fasta? ...
written 6 days ago by Sej Modha2.3k
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Comment: C: Transcription Start Site for bacteria
... Not sure if you have already seen this but a range of tools is available on [OmicsTools][1] that include bacterial specific tools such as [FGENESB][2]. [1]: https://omictools.com/promoter-prediction-category [2]: http://www.softberry.com/berry.phtml?topic=fgenesb&group=programs&subgrou ...
written 7 days ago by Sej Modha2.3k
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Answer: C: Biopython / Python for genomics data analysis online courses
... Did you have a look at [Coursera courses,][1] not sure if there are specific bioinformatics courses but data science ones might be a good starting point. EDIT: I forgot to mention that [GOBLET][2] would be something to look at for the bioinformatics orientated courses. [1]: https://www.courser ...
written 12 days ago by Sej Modha2.3k

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Scholar 29 days ago, created an answer that has been accepted. For A: CAR parameters not work
Scholar 29 days ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 5 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
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Scholar 8 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
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Scholar 4 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 4 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Scholar 5 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Appreciated 6 months ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
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