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Recent Replies
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
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GenoMax
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OP is working with long reads so the chances of reads aligning to unlocalized scaffolds are relatively small. Doing some testing may be suf…
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I personally think that comparing the same peak between conditions is meaningful and comparing peaks within the same sample is not.
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These regions are present in the genome and removing them might incorrectly redirect alignments to known genes. I don't see why you would r…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
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Ok thank you! Do you know if there is an easy way of doing so with ncbi-genome-download or I need to use another tool?
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Redirection of Duplicate PMIDs
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dominickd
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The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
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The `-d` sorting mode does the entire sort in memory, so it will only work if you have enough memory to load your whole GAM file.
To fin…
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I have a list of PMIDs for publications linked to a list of grants, exported from NIH RePORTER.
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
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Yes you can remove those if you are only interested in annotated genes.
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[This could help][1]
[1]: https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Trinity-De-novo-Transcriptome-Assembly-W…
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Are you sure you have looked into the HiFiasm output files (fasta and GFA) in detail and excluded non-primary contigs, hap1, hap2 and other…
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You can use seqtk to find gaps in a fasta
https://github.com/lh3/seqtk
seqtk gap
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Can you post a screenshot of what you are referring to? Why did you choose to "clean" your data?
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