Moderator: Sej Modha

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Sej Modha3.1k
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Glasgow, UK
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http://bioinformatics....
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SejModha
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2 days, 12 hours ago
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Posts by Sej Modha

<prev • 500 results • page 1 of 50 • next >
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Comment: C: Conversion of Fasta file
... As previous comments and answers have mentioned, it is not possible to convert a FASTA file to a FASTQ file without quality score information, however, you can always append dummy quality scores, but it is not advisable, especially if you are planning to deposit the data in public repositories. On ...
written 2 days ago by Sej Modha3.1k
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Comment: C: solution for SPades to assemble genome with low quality data
... Is this single-cell, iontorrent data? Why are you using --sc tag with --iontorrent? How big is your data file? Can you provide more memory for this process? ...
written 3 days ago by Sej Modha3.1k
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Comment: C: solution for SPades to assemble genome with low quality data
... Hello StudentBio, Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. Thank you! ...
written 3 days ago by Sej Modha3.1k
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Comment: C: Remove sequences without alignment in mummerplot
... Did you try `--filter` in `mummerplot`? ...
written 4 days ago by Sej Modha3.1k
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Comment: C: What is required for genome annotation?
... Hi there, Could you please provide more information about the data What stage is the genome assembly? e.g. scaffolds or draft genome? Is it a new species or a new strain of fungi? Is there an annotated genome of close species/strain available? Although I am not an expert in fungal bioinforma ...
written 5 days ago by Sej Modha3.1k
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Comment: C: TopHat v2.1.1- Warning: TopHat did not find any junctions in GTF file
... I'd suggest that you should use HISAT2 or STAR instead of TopHat2. https://www.biostars.org/p/230724/ ...
written 5 days ago by Sej Modha3.1k
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Answer: C: Is there any quick way to annotate KO terms using a script or tool?
... If you paste the list of KO IDs in the text box provided on https://www.genome.jp/kegg/ko.html and search for 'Get title' it should return the annotations. ko:K13457 RPM1, RPS3; disease resistance protein RPM1 ko:K03233 EEF1G; elongation factor 1-gamma ko:K00430 E1.11.1.7; per ...
written 5 days ago by Sej Modha3.1k
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Comment: C: Orienting contigs/ scaffolds in de novo assembly
... There is a range of contig reordering tools available: - [ABACAS][1] - [Mauve][2] However, if you're already using Mummer, then you could look into the [show-tiling][3] option as it can also fix order and orientation and can generate a pseudo-sequence when `-p filename Output a pseudo molecul ...
written 11 days ago by Sej Modha3.1k
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Comment: C: Convert .gprobs files to PLINK format
... Hi @lauretomas, Do you reckon any tools/scripts described in the previous post would help? https://www.biostars.org/p/17943/ ...
written 11 days ago by Sej Modha3.1k
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Comment: C: BioPython local blast different results than blast+ local blast
... Maybe top BLAST hits were not in the same order? You could get output in the tabular BLAST format using `-outfmt 6` option and parse the hits for each query and check if it is just the order that was different or there were discrepancies in the corresponding evalue and bitscore. ...
written 12 days ago by Sej Modha3.1k

Latest awards to Sej Modha

Teacher 16 days ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Commentator 16 days ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R
Commentator 19 days ago, created a comment with at least 3 up-votes. For C: Help with ggtree tip labeling in R
Scholar 27 days ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Scholar 4 weeks ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Appreciated 3 months ago, created a post with more than 5 votes. For A: NCBI Protein GI to Genome Accession
Scholar 4 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: NCBI Protein GI to Genome Accession
Appreciated 4 months ago, created a post with more than 5 votes. For A: 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: NCBI Protein GI to Genome Accession
Popular Question 5 months ago, created a question with more than 1,000 views. For NCBI Protein GI to Genome Accession
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Scholar 8 months ago, created an answer that has been accepted. For A: CAR parameters not work
Scholar 8 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 8 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 8 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 9 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file
Scholar 9 months ago, created an answer that has been accepted. For A: Convert GTF file into GFF3 file

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