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Recent Replies
Comment: R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
by
TC_Chang
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10
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
by
dthorbur
▴
830
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 …
Answer: How can I map coordinates between two strains of yeast?
by
dthorbur
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830
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, […
Comment: Identify clusters of populations based on gene expression
by
Nitin Narwade
★
1.5k
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…
Answer: The difference blastn output when using subject and db options
by
GenoMax
136k
Default `task` option is `megablast` for `blastn` which looks for `highly similar sequences` compared to `blastn` which is looking for `som…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
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:
by
barslmn
★
2.0k
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…
Comment: Python function to export the annotated records to genbank file using python and
by
barslmn
★
2.0k
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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