Moderator: Asaf

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Asaf7.0k
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Israel
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8 years, 10 months ago
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Posts by Asaf

<prev • 955 results • page 1 of 96 • next >
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Answer: A: KEGG pathways associated to a gene using BiomaRt
... I know it's an old question but wanted to update that `kegg_enzyme` was added to the list of attributes in bioMart, it will return the pathway (the number portion of mapXXXXX pathway) and the enzyme EC number. try(ensembl <- biomaRt::useMart("ensembl", dataset = "mmusculus_ge ...
written 2 hours ago by Asaf7.0k
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Comment: C: bcl2fastq results in Poly-N in R1
... Do you have access to the library QC? (pre-sequencing) ...
written 4 hours ago by Asaf7.0k
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Answer: A: Cutdapt for batch processing ?
... Use pipeline management system like nextflow, snakemake or wdl/cromwell. And make sure you have to actually use cutadapt. If your next step is mapping to the genome you're probably good without removing adapters. ...
written 1 day ago by Asaf7.0k
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Answer: A: How to get 1 top hit only for each query in blastx
... The max_hsps never really worked properly, they have some explanation for this if I recall. You can use sort to do that: sort -k1,1 -k11,11g CDS_blast.txt | sort --merge -u -k1,1 This will sort by query sequence and p-value (assuming default format 6 output), then will select the first result ...
written 1 day ago by Asaf7.0k
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Comment: C: Generate count table using Samtools
... Count table of what? Reads mapped to each gene? contig? ...
written 1 day ago by Asaf7.0k
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Comment: C: 10 years a bioinformatician: some reflections
... A great read! Loved the part about the imposter syndrome, it takes time to realize and accept that. ...
written 1 day ago by Asaf7.0k
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Answer: A: Creating assembly graphs .gfa
... These files are generated in the assembly process using software like e.g. flye. Usually assemblers do the process of reads -> assembly graph -> assembly (contigs or scaffolds). The graphs are intermediates and represent repeats and branches, basically uncertainties in the assembly process. Y ...
written 1 day ago by Asaf7.0k
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Comment: C: The Tophta2 ERR, [ERRno 2]
... This post requires some formatting. Please don't use the answer to add more data, you can add a comment or edit your post. As for your question, the names of the files you gave bowtie2 to write the output to contain weird directories that don't exist, please check your command. ...
written 2 days ago by Asaf7.0k
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Comment: C: seqmule gatk vcfv4.2 error
... What was the command line? How does the input look like? ...
written 6 days ago by Asaf7.0k
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Comment: C: Use pre-assembled paired-end reads as single-end for metagenome assembly with me
... Do reads from (1) contained in (2) or they are two different groups? You have quite a mess there as reads are usually in fastq format, you should probably start the assembly from scratch. There are good assembly pipelines out there that start with the raw fastq files. ...
written 6 days ago by Asaf7.0k

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Scholar 1 day ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
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Scholar 8 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
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Scholar 10 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?

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