Biostar Latest

1,000 results • Page 3 of 20

votes

replies

19k

views

17 follow

pathway database subjective

updated 4 months ago by Peter Karp ▴ 30 • written 13.1 years ago by Shigeta ▴ 470

votes

replies

7.3k

views

13 follow

Popular Question to Tao ▴ 30

Recent Replies

Comment: R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales by TC_Chang ▴ 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 ▴ 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.

Traffic: 2269 users visited in the last hour

Content Search
Users
Tags
Badges

Help About
FAQ

Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

version 2.3.6