Moderator: Sej Modha

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Sej Modha3.6k
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Glasgow, UK
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SejModha
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Posts by Sej Modha

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Comment: C: Plot factors by specific column in ggplot
... If it is a generic order thing in ggplot2 checkout https://kohske.wordpress.com/2010/12/29/faq-how-to-order-the-factor-variables-in-ggplot2/ ...
written 10 hours ago by Sej Modha3.6k
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Comment: C: When converting a GFF3 file into a EMBL file, what should be filled as locus_tag
... Please see the [Parameter][1] section of the tool manual for more info. [1]: https://github.com/NBISweden/EMBLmyGFF3#parameters ...
written 11 hours ago by Sej Modha3.6k
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Comment: C: Error in aligning bowtie index files with ebwtl format while running tophat
... Hello divchauhan07, You should know that the old 'Tuxedo' pipeline of Tophat and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: [Transcript-level expression an ...
written 11 hours ago by Sej Modha3.6k
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Comment: C: best programs for alignment of large whole genomes?
... I had used [Synima][1] recently for syntenic comparison of multiple Plasmodium genomes and thought that it produced nice figures too. [1]: https://github.com/rhysf/Synima ...
written 4 days ago by Sej Modha3.6k
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Comment: C: BLAST multiple database against each other
... What kind of BLAST searches is being performed? If it is BLASTP or BLASTX then you can use [DIAMOND][1] as it is much faster than BLAST. [1]: https://github.com/bbuchfink/diamond ...
written 5 days ago by Sej Modha3.6k
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Comment: C: Map plasmodb gene ID to pdb crystal structure if exist
... I'd suggest sticking to PlasmoDB results as it is regularly updated and maintained by a dedicated team of the software developers. It is highly likely that genome sequences and annotations on NCBI may not be as updated as PlasmoDB. ...
written 5 days ago by Sej Modha3.6k
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Comment: C: Encountered internal Bowtie 2 exception (#1) bowtie2-align exited with value 1
... I meant that individual commands should be run to process each sample separately. Please see http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#paired-inputs for more info. e.g. `bowtie2 -x ref_index -1 file_1.fq -2 file_2.fq -S output.sam` On another note, why did you use rna-seq tag? Is this ...
written 6 days ago by Sej Modha3.6k
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Comment: C: Encountered internal Bowtie 2 exception (#1) bowtie2-align exited with value 1
... Are you trying to align all fastq files using this one command? It looks like you have paired-end data, are these meant to be paired-end files? `"/home/luz_garcia_longoria/workspace/s23_1.fq", "/home/luz_garcia_longoria/workspace/s23_2.fq" ` The error that you are getting here is specifically re ...
written 6 days ago by Sej Modha3.6k
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Comment: C: Encountered internal Bowtie 2 exception (#1) bowtie2-align exited with value 1
... Hi there, Could you post your script here? It looks like some parameter that you may have used to pass file name is empty. In bowtie2 commands filenames are .fasta and .fq which should be`filename.fasta` or `filename.fq` `bowtie2 --threads 4 --local --no-unal -x /home/luz_garcia_longoria/workspace ...
written 6 days ago by Sej Modha3.6k
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Answer: A: Problems with extracting genes from a genbank file using biopython
... Hi There, I have used a sample genbank file here, the following should work for you too. https://gist.github.com/sejmodha/cf482f4d28cc77941fa379fc4e99fb6f This produces following output. ['335:4642', '335:1838', '4586:5165', '5104:5396', '5376:7970', '5515:8199', '5607:5856', '5770:8341', '6 ...
written 7 days ago by Sej Modha3.6k

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Teacher 11 days ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
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