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1500 questions
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2 answers

What is the best Query to retrieve DNA from NCBI?

I want to retrieve a sequence for many species from the Nucleotide database in NCBI. I'm using a command line approach and I have to figure out what is the best query that will return exclusively the region of DNA I am interested in and filter out…
Mirko
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how to install cibersort in R, to do deconvolution using my RNA-seq Data with public single cell data

I have RNA-seq Data from lung cancer immunotherapy patients but i don't have any single cell data from my sample, so i wanted to do a deconvolution with a public single cell data. I thought of doing the analysis with the cibersort website plataform…
Rita Soares
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1 answer

Discrepancy with featurecounts analysis using a forward stranded and reverse stranded protocol

My RNAseq analysis pipeline is as follows: fastqc (read quality is good, some overrepresentation of adaptor sequence) → trimmomatic (trimmed adaptor sequence, qc report after trimming suggests the overrepresented adaptors are gone) → HISAT2 (used a…
xtian
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Cannot obtain alignment summary after running Bowtie2

I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following: ## Time loading reference: 00:00:00 ## Time loading forward index:…
ALEJANDRA PANDO CACIANO
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1 answer

GWAS in python?

A question similar to this has also been asked on Biostars I understand GWAS is done with R, but are any written in Python? I'm used to python and java, acclimating to R will take a bit of time and my advisor wants some data analyzed. I plan on…
Katherine
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1 answer

How can I export a pruned phylogenetic tree in nexus format in R?

I have a phylogenetic tree with a lot of different populations and I wanted to removes most of them and apply new names to the labels. I wrote this code: library(ape) library(phylotools) tree<-…
Nickmofoe
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1 answer

how to add a custom elements into PyMOL visualization?

I would like to add some 3D elements (balls and lines) to the PyMOL visualization to highlight some "holes" in the structure. Say I fetch 1tqn and I want to add a yellow ball somewhere (to specific coordinates, say [-19, -23, -14]) in the view. Or a…
jhutar
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1 answer

What database do gene IDs starting with sp_v2 refer to?

I am a student trying to analyze GEO2r datas for one of my courses. The IDs given in the output are different for different series. I need to convert all of them to a similar format. In this process I encountered the following type of ID which I…
hhoomn
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How can I convert my tree to the correct nexus format?

I would like to use the program BayesTraitV4. I have my phylogenetic tree in NEXUS format but the program does not accept it. I checked the example data and while they are also in NEXUS format, they seemed different. I will provide a part of my data…
Nickmofoe
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Generating CIGAR strings for MSA with reference

I have a list containing the results of a MSA: msa = [ '-G-ATG-CGGATACCG-', # reference sequence 'CGTATCTCG--TACCGA', '-GTATCTCGT-GACCG-', 'CG-AT--CGG-GACCGA', '---AT--CG--GACCGA', '-GTAT---GC-GACCG-', …
Fravadona
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3
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1 answer

Shell script to validate fastq issue

I have two GSM ID as test case where both of them are having data when I checked through sra explorer tool but when I try to fetch through a script only one of them returns output where the other one fails. GSM ID GSM3603268 GSM2683458 Output For…
kcm
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2 answers

efetch multiple records at once

If I want to efetch two records, I can do the following: efetch -db nuccore -id AB610939,AB610940 -format fasta I have hundreds of records to fetch. Can I put all the IDs in a file and efetch. If so, how?
Supertech
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1 answer

Trimmomatic QC report shows drop in the reads and presence of overrepresented sequences

This question was also asked on Biostars I am performing a de novo genome assembly using Illumina paired-end short reads, sequenced on a NovaSeq X by our collaborator at UCLA. At present, I am in the stage of trimming the adapters. Here, you can…
Vijith Kumar V
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3
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2 answers

Remote NCBI's Blast Perl API: maximising hits returned via command line

Question and Background I'm using NCBI's Blast Perl API to interrogate Genbank for example blastp. I don't get the throughput using their point and click web stuff. I tried Biopython's Bio.Blast import NCBIWWW but its under access restrictions from…
M__
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1 answer

Error output in nextflow pipeline using fasterq-dump

I have one file with multiple SRA accession called Dataframe_with_accession.txt, for this example I just put one SRA in that file called :SRR8933535 And the idea is to create a nextflow pipeline to download the sra files in the…
Grendel
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