User: Sej Modha

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Sej Modha2.0k
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Glasgow, UK
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http://bioinformatics....
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SejModha
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3 years, 10 months ago
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Posts by Sej Modha

<prev • 286 results • page 1 of 29 • next >
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Answer: A: Mapping contigs & scaffolds to ref genome?
... Bowtie2 is a short read mapper and is not suitable for such application, [BLAT][1] or [MUMMER][2] would be more suitable in such cases. [1]: https://genome.ucsc.edu/FAQ/FAQblat.html [2]: http://mummer.sourceforge.net/ ...
written 10 hours ago by Sej Modha2.0k
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Comment: C: reordring contigs in Mauve
... You could use command line version instead: java -Xmx500m -cp Mauve.jar org.gel.mauve.contigs.ContigOrderer -output results_dir -ref reference.gbk -draft draft.fasta Is this a follow up question from https://www.biostars.org/p/278149/ ...
written 1 day ago by Sej Modha2.0k
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Comment: C: Subtracting one BAM [control] from another BAM [sample].
... Two possible output formats for bamCompare are bedgraph and bigwig. ...
written 1 day ago by Sej Modha2.0k
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Answer: A: Subtracting one BAM [control] from another BAM [sample].
... [bamCompare][1] from deepTools can help. [1]: http://deeptools.readthedocs.io/en/latest/content/tools/bamCompare.html ...
written 1 day ago by Sej Modha2.0k
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Answer: A: Denovo assembly of bacterial genome
... [Mauve][1] can be used to reorder contigs. You can also use a reference guided scaffolder such as [scaffold builder][2] to generate a draft genome assembly [1]: http://darlinglab.org/mauve/user-guide/reordering.html [2]: http://edwards.sdsu.edu/scaffold_builder/ ...
written 1 day ago by Sej Modha2.0k
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Comment: C: Best Blast Hits from Tabular Outputs in Multiple files
... You could create a new directory with all BLAST results file and change the path in the script to that folder as blastdir. ...
written 5 days ago by Sej Modha2.0k
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Comment: C: Best Blast Hits from Tabular Outputs in Multiple files
... I am unable to find the script that you have provided the link to but from looking at the code it looks like it's the blastdir issue as it is hard-coded in the script. Either you can change that location to where the blast results are on your computer or you could try https://github.com/alunem/bioma ...
written 6 days ago by Sej Modha2.0k
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Comment: C: combining quantification (featureCounts) result files into a single dataset
... You can merge multiple dataframes by rownames assuming that unique geneids are defined as rownames. https://stackoverflow.com/questions/7739578/merge-data-frames-based-on-rownames-in-r ...
written 6 days ago by Sej Modha2.0k
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Answer: A: definition of N50 in trinity
... [What Does The "N50" Mean?][1] [1]: https://www.biostars.org/p/723/ ...
written 6 days ago by Sej Modha2.0k
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Comment: C: combining quantification (featureCounts) result files into a single dataset
... FeatureCounts can take multiple alignment files as input. featureCounts [options] -o counts.txt file1.bam file2.bam file3.bam ...
written 6 days ago by Sej Modha2.0k

Latest awards to Sej Modha

Appreciated 6 days ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Scholar 6 days ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: NCBI Protein GI to Genome Accession
Scholar 9 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 10 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Appreciated 3 months ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Scholar 3 months 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: Where is the source code for legacy BLAST?
Scholar 4 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Appreciated 4 months ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Student 5 months ago, asked a question with at least 3 up-votes. For NCBI Protein GI to Genome Accession
Scholar 5 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Where is the source code for legacy BLAST?
Guru 8 months ago, received more than 100 upvotes.
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Where i can find complete genome of any organism?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Where i can find complete genome of any organism?
Teacher 8 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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