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Comment: Construction of single sequence assembly out of contigs
Answer: featureCounts results: low rate of 'Successfully assigned alignments'
The Biostar Herald for Monday, November 27, 2023
Comment: use bioservices.UniProt (python) to map uniprot accession to [multiple] ensembl
Answer: Best practices for unstranded sequences in featureCounts
Answer: DEseq2 input
Comment: Filter out ALT contigs from CRAM
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Recent Replies
Comment: R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
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TC_Chang
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Hi jv, Thank you for your reply. Basically, I'm trying to generate the figure shown below with two different y-axis scales. Any suggestio…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
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dthorbur
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I don't have a suggestion for low yield DE analyses, but I am curious about the samples. Did you conduct any ribo-depletion steps prior to …
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dthorbur
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It sounds like you are looking for synteny between the two genomes. I'm assuming they are assembled, but that may not be the case. If so, […
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Nitin Narwade
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Why don't you just plot it on your UMAP If it is specific to one cluster/sub-population you should get a relatively high expression in that…
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Default `task` option is `megablast` for `blastn` which looks for `highly similar sequences` compared to `blastn` which is looking for `som…
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https://www.biostars.org/u/14684/ may comment on this but it may be the order of operations that is causing this. After the `tpe` is applie…
Comment: Construction of single sequence assembly out of contigs
by
colindaven
5.7k
Inspector (only for long reads) and Merqury for short reads are also pretty good methods for doing a QC of your assembly.
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
GenoMax
136k
> why I have soo many multimapping reads? That is a characteristic of the libraries. Not much you can do at this point in process. Just ha…
Comment: unicycler error : [Errno 13] Permission denied:
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barslmn
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This is not really a bioinformatics question. Either you're not the owner or in the group of the directory or the directory don't have wr…
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barslmn
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Could you paste the error as printed to your screen?
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
I have found dedup.sh script of bbmap tool that removes duplicated sequences. Also there is a seqtk tool. Is it safe to remove duplicated s…
Comment: featureCounts results: low rate of 'Successfully assigned alignments'
by
Hamtaro
▴ 10
Thank you for your reply. I how can I identify why I have soo many multimapping reads? The samples comes from blood from patients under d…
Comment: Construction of single sequence assembly out of contigs
by
analyst
▴ 10
Honestly I have not assessed duplication after assembly. However I used trimmomatic for data filtration before assembly. Trimmomatic param…
Answer: featureCounts results: low rate of 'Successfully assigned alignments'
by
kvn95ss
▴ 20
I could see the following clues from - hisat2 - ```23026867 (61.37%) aligned concordantly >1 times``` And from featureCounts - ``` Mu…
Comment: CPTAC data, download, merge
by
Mohita
▴ 50
I am also facing the same problem. I will be grateful if you help me out for this.
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