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Comment: Failed kmer content
Using vg gamsort with naive sorting algorithm
Answer: Using vg gamsort with naive sorting algorithm
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Comment: Downsampling fastq file
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
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Recent Replies
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Ok! I have a recommendation. I'll submit it as an answer, pending your feedback. vincent
Comment: DYH17 Structure Prediction
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anasjamshed
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In modeller we need to use templates as well.
Comment: DYH17 Structure Prediction
by
Ram
43k
Mensur said > The latter option assumes you know how to use Modeller Do you know how to use Modeller? I vaguely recall there being a mini…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
OP is working with long reads so the chances of reads aligning to unlocalized scaffolds are relatively small. Doing some testing may be suf…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
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ATpoint
81k
I personally think that comparing the same peak between conditions is meaningful and comparing peaks within the same sample is not.
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
ATpoint
81k
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?
by
njornet
▴ 20
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?
Comment: Using vg gamsort with naive sorting algorithm
by
Pierre Lindenbaum
161k
> 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
by
dominickd
• 0
The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
Answer: Using vg gamsort with naive sorting algorithm
by
anovak
▴ 120
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…
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I have a list of PMIDs for publications linked to a list of grants, exported from NIH RePORTER.
Comment: Plot DNA methylation level of DMR on the basis of certain genes
by
Pierre Lindenbaum
161k
> 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: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
Yes you can remove those if you are only interested in annotated genes.
Comment: Help for coding: Trinity for differential gene expression studies
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mchour
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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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colindaven
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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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