Community Digest

Top new questions this week:

Comparing sequence similarity of two sets of peptide sequences?

What tools can we use to compare two sets of peptide sequences? The biological question is I have some kmer sequences of some proteins and would like to know how similar are these kmer sequences ...

blastp peptide  
user avatar asked by Johnny Tam Score of 2
user avatar answered by darked89 Score of 2

Single Node Deletion in Cheng and Church Algorithm

Cheng and Church Algorithm is a biclustering algorithm or an unsupervised learning task with which both rows and columns in a data matrix can be placed in concurrent clusters. In the original paper, ...

python machine-learning algorithms  
user avatar asked by ShokofehVS Score of 2
user avatar answered by M__ Score of 0

Assertion `compressBound(0xff00) < 0x10000' failed when using STAR 2.7.9a

This question was also asked on github I am using STAR 2.7.9a. In the last two days, I am getting an error when running alignments with STAR (independently from the data and genome index I am using). ...

rna-alignment star  
user avatar asked by RobAlbn Score of 2
user avatar answered by John Marshall Score of 3

How to visualize unique and overlapping genes in upSet R plot

I am still a newbie in the field of bioinformatics. I have been attempting to visualize unique and common genes across six different tissues using the UpSetR plot ...

r upsetr  
user avatar asked by S'bonelo Glen Khumalo Score of 2
user avatar answered by darked89 Score of 2

How to parse hmmsearch output?

I did hmmsearch with --notextw and --domtblout and I see several results for ids, I want to ...

linux biopython functional-annotation parsing hmmer  
user avatar asked by bobr Score of 1
user avatar answered by darked89 Score of 2

Can alphafold 2 be used to identify residues important for binding?

I am interested in using AlphaFold2 to identify residues within a homodimer that are important for the protein-protein interaction. I have been able to use ColabFold to produce a predicted dimer ...

alphafold  
user avatar asked by user48660 Score of 1

Multi Factor in Deseq2 Gene enrichment analysis

I want to see how the gene expression differs in breast cancer between three species, and I am using DESeqDataSetFromMatrix on my count table. ...

sequence-analysis deseq2 gene-expression go-enrichment  
user avatar asked by ToTheMoon Score of 1
user avatar answered by swbarnes2 Score of 2

Greatest hits from previous weeks:

Remove/delete sequences by ID from multifasta

I have a fasta file like this: >Id1 ATCCTT >Id2 ATTTTCCC >Id3 TTTCCCCAAAA >Id4 CCCTTTAAA I want to delete sequences that have the following IDs. <...

fasta awk shell benchmarking  
user avatar asked by andresito Score of 9
user avatar answered by user172818 Score of 7

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

What are the actual differences between different annotation databases? My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation)...

sequence-annotation ensembl refseq gencode  
user avatar asked by Plasma Score of 46
user avatar answered by Mitra Score of 24

Error in seaborn plot " Horizontal orientation requires numeric `x` variable"

I am trying to plot a box plot with seaborn with the following code ...

visualization python graphs  
user avatar asked by Megha Score of 4
user avatar answered by M__ Score of 3

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it... ...

phylogenetics sequence-alignment fasta phylogeny covid-19  
user avatar asked by Rebecca J. Stones Score of 191
user avatar answered by Cody Gray - on strike Score of 163

How can I downsample a BAM file while keeping both reads in pairs?

I know how to downsample a BAM file to lower coverage. I know I can randomly select lines in SAM, but this procedure can't guarantee two reads in a pair are always sampled the same time. Is there a ...

sam  
user avatar asked by medbe Score of 19
user avatar answered by rightskewed Score of 17

How to calculate p-values for fold changes?

I'm currently working with data from a Luminex multiplex assay. In this assay, the concentrations of 17 different analyte proteins were identified in 12 groups in triplicate. One of these 17 groups ...

statistics  
user avatar asked by J0HN_TIT0R Score of 3
user avatar answered by Ian Sudbery Score of 4

How to subset a BAM by a list of QNAMEs?

I have a text file 'qnames.txt' with QNAMEs in the following format: EXAMPLE:QNAME1 EXAMPLE:QNAME2 EXAMPLE:QNAME3 EXAMPLE:QNAME4 EXAMPLE:QNAME5 I would like to ...

sam samtools  
user avatar asked by EB2127 Score of 8
user avatar answered by Bioathlete Score of 4

Can you answer this question?

Calculating Fisher's exact test for COG categories

This is a continuation of the following question - Fisher's exact test for COG categories in pan, core genome analysis Also, the dataset - How do I perform a Fisher's exact test on this data to ...

statistics eggnog pangenome  
user avatar asked by K_081 Score of 2
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