User: colindaven

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colindaven1.9k
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Posts by colindaven

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Comment: C: Generate count table using Samtools
... Try a newer version of samtools like 1.7+ The you can do what @lieven.sterck recommended above, maybe idxstats will be most helpful. Program: samtools (Tools for alignments in the SAM format) Version: 1.7 (using htslib 1.7) Usage: samtools [options] Commands: ...
written 15 hours ago by colindaven1.9k
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Answer: A: how to find haplotype of SNPs
... If you have short reads (eg not Pacbio/Nanopore) phasing results are likely to be very, very poor, as no long range information (long reads) are available. ...
written 1 day ago by colindaven1.9k
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Answer: A: Variant calling on Nanopore reads
... Clair also has a good reputation in addition to Longshot https://www.biorxiv.org/content/10.1101/2020.02.07.939322v1?ct= However I have Longshot https://github.com/pjedge/longshot quite easy to install and run, as long as you can get over the initial RUST hurdles. Fascinatingly, it's the first tool ...
written 1 day ago by colindaven1.9k
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Answer: A: Maker usage and tBLASTn
... Maker is good - but as lieven.sterck says, it is a genome annotation program. It does work and is not too tricky to configure. Do you want to annotate a genome and create a geneset ? ...
written 1 day ago by colindaven1.9k
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Comment: C: Generate count table using Samtools
... You have included almost no information in your post so it is impossible to help you. Retry ? What did you align to ? Did you align data ? ...
written 1 day ago by colindaven1.9k
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Comment: C: Indexing Genome Commands in Linux (hummingbird-ucsc)
... You may not have enough RAM (how much do you have ?). Use `htop` or `free -g` to find out. If you don't have enough, the mapping step might also not work. ...
written 10 days ago by colindaven1.9k
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Comment: C: install bcl2fastq
... Try creating a file like this globalenv and adding it to your /home/YOURUSER/.bashrc file eg at the end of my .bashrc file I write this: $ cat ~/.bashrc source /mnt/ngsnfs/globalenv/globalenv For more details check https://unix.stackexchange.com/questions/26047/how-to-correctly-add-a-path-to-pa ...
written 14 days ago by colindaven1.9k
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Comment: C: Methods to convert SOLiD reads to nucleotide space
... Yep, it works, yep, they should use other data - but that wasn't the question. I'd probably trust it for alignments, but not for SNV calls as you're not using the colour space information. ...
written 15 days ago by colindaven1.9k
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Comment: C: install bcl2fastq
... For the second question, you need to add bcl2fastq to your PATH, eg something like https://askubuntu.com/questions/60218/how-to-add-a-directory-to-the-path ...
written 15 days ago by colindaven1.9k
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Answer: A: Methods to convert SOLiD reads to nucleotide space
... Because the reads were aligned against a reference, you can just use BAM 2 fastq methods to extract the sequences. That way you get a FASTQ and avoid colourspace altogether, which I would not recommend using for RNA-seq projects in any case. You can use a modern samtools for this: samtools fa ...
written 15 days ago by colindaven1.9k

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