Hi,
I have some normalized BigWig files and now I want to convert these normalized BigWig files to count matrix. Can anyone give me any advice? I will appreciate
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i am using rmats software, here i have settled all dependencies. now i am facing problem in input file, mainly how to arrange bam file in txt file. so here i have different species bam file and gtf file also. there confusion in...b1 and b2 during run file if i have 1 species and 1 gtf filw then how can add species to during rtunning time. if i am wrong then guide me to make a correct...input file…
for that, I require their DNA sequencing reads. I believe I can obtain these reads from their CRAM files of the normal samples, so I downloaded a slice of the CRAM according to their instructions
bin/score-client view --object...id 28358cf3-fba0-51a3-8b93-104bd5d48b23 --reference-file /home/victor/ref-fasta/GRCh38_full_analysis_set_plus_decoy_hla.fa --output-dir /media/victor/c1d5c312-b546-…
Good morning,
I aim to chop an already aligned bam file based on different regions of a gene as follow:
samtools view -b -o out.bam -L regions.bed origin.bam
samtools sort -o out.sort.bam...out.bam
samtools index
Then I want to convert the `out.bam` into two unaligned FASTQ files (each member of the read pair parsed to one of the two files) using SamToFastq:
…
updated 4 hours ago • Lila M
working with two lanes of Hi-C reads (2 forward, 2 reverse). Initially, I was merging the raw FASTQ files before mapping, but I've since been mapping each set of forward and reverse reads independently with BWA-MEM2 and then...merging the BAM files. I've also tried using only a single lane of forward and reverse reads.
2. Initially, I deviated from the VGP pipeline and
updated 7 hours ago • Winter
Hello, how do I import a fastq file from my local windows computer into fluent terminal wls
updated 7 hours ago • oumo
base)
I'm not sure how to interpret this - I assume that some internal python3 file is missing or not found. Possibly pycostat, given the SAT solver errors in installing and creating environments?
conda...install -c conda-forge biopython # code to generate error
/opt/homebrew/Caskroom/miniforge/base/lib/python3.10/site-packages/conda_package_streaming
I haven’t been able to solve with my program:
“Identify all ORFs present in each sequence of the FASTA. What is the length of the longest ORF? What is the identifier of the longest ORF. For a given identifier, what is the longest...longest ORF in that identified sequence? Idenfity all repeats in a sequence for all sequences in the FASTA, along with how many times each repeat occurs and which is t…
I have some very large WGS BCF files and I would to extract just the first 8 columns, thus reducing to just a 'sites-only' VCF/BCF.
Does BCFTOOLS have a canned...I have some very large WGS BCF files and I would to extract just the first 8 columns, thus reducing to just a 'sites-only' VCF/BCF.
Does BCFTOOLS have a canned option...t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO\n"
but I'm finding t…
updated 15 hours ago • Matthew
Hello,
I'm annotating a vcf file using ensembl vep and gnomad v4 vcf file:
vep --cache --offline --species homo_sapiens --assembly GRCh38 \
--input_file input.vcf...Hello,
I'm annotating a vcf file using ensembl vep and gnomad v4 vcf file:
vep --cache --offline --species homo_sapiens --assembly GRCh38 \
--input_file input.vcf \
--custom gnomad.vcf.b…
Hello all,
Data: Paired end, RNASeq data.
I had an issue with the featureCounts output Assigned reads are greater than the HISAT mapped on aligned concordantly exactly 1 time
```
From HISAT:
aligned concordantly exactly 1 time is 48335140
From featureCounts summary:
Assigned: 64074047
```
Assigned value is 1.32 times greater than HISAT mapping results. It's weird that Assigned value is hig…
updated 17 hours ago • Prawesh
Hi there,
I am working on the de novo analysis of bacteria. This bacteria is related to Bacillus paranthracis, which was identified using rMLST, TYGS, and BLAST analysis. The genome assembly file was then provided to the KEGG-KASS tool. Although the prokaryotic dataset was selected for analysis, the identified KO...paranthracis, which was identified using rMLST, TYGS, and BLAST analysis. The ge…
Hello everyone,
I'm currently working with VCF files of mutations from the TCGA dataset using the hg38 assembly.
To further my analysis, I'm interested in comparing mutation
updated 21 hours ago • elisheva
my current experience in IT financial system support
got certification in bioinformatics and python/biopython
updated 1 day ago • shehab
fetus (the one inherited from the mother by the fetus). The final results I'm looking for are a bam file with the reads from the unique chromosome of the mother, another with the reads from the unique chromosome of the child
updated 1 day ago • njornet
Hey everyone
I need some help with SAMtools (v 1.3.1) and such. I have 2 files that I want to align, with the ultimate goal of understanding what percentage of the reference genome is covered by...Hey everyone
I need some help with SAMtools (v 1.3.1) and such. I have 2 files that I want to align, with the ultimate goal of understanding what percentage of the reference genome is covered by…
Dear all,
I need bed files for **admixture** and **map** files for **beagle imputation** for **polyploid** plant. I tried through **Plink** but it do not support polyploid...extra-chr** flag to run it anyway, I observed **0s** in third row of output **.bim** and **.map** file.
Your help will be highly appreciated
no cost after careful evaluation.
1. [TenDna][1]
TenDna allows you to free uploading DNA test data file 23andMe, AncestryDNA, FamilyTreeDNA, MyHeritage and receiving extended personalized report on health and wellness...and variants.
To generate your personalized genetics report, Promethease scans your raw data file, identifying the specific variants of certain genes you possess. It then match…
Hi, I wonder how the samtools consensus work without explicitly pointing out the reference genome. If I intend to add a reference genome to generate the consensus sequence, is it possible based on samtools? Thanks a lot.
Reference: https://www.htslib.org/doc/samtools-consensus.html
Get the file for this array task
FILE=${input_files[$SLURM_ARRAY_TASK_ID]}
# Extract the base name of the file (without the directory and...extension)
BASENAME=$(basename "$FILE" _trimmed.fq.gz)
# Print the basename
echo "Processing file: $BASENAME"
# alignment
STAR --runThreadN 12 \
--readFilesCommand...zcat \
--readFilesIn $FILE \
--genomeD…
Hello,
I am relatively new to the field of bioinformatics and I am currently working on a small program which should, among other things, filter a multisample VCF file for all genotypes except one of them. Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes...I am currently working on a small program which should, among other things, filter a multisample V…
everyone,
I tried to map paired end reads to reference the genome using BWA-MEM and I got SAM file. When I sort my SAM file with SAMtools, I got this error:
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation
results with only 581 barcodes in the whitelist with but over 1700 barcodes are written to the `tsv` file with the knee method.
Is there a reason for this big difference?
I was wondering how I can figure out why I have such aa low...number of barcodes. My fastq file has almost 20Mil reads and I expected more barcodes (these list is of over 18K unique barcodes).
thanks
Assa</umi_1>…
updated 2 days ago • Assa Yeroslaviz
Dear scientists,
I have to impute my variants (combined VCF file of multiple samples).
I found Beagle tool for imputation in linux. I don't have idea about **reference panel file why it is important
updated 2 days ago • analyst
I'm using `bbduk` to count a specific pattern in my fastq file. The pattern is quite long and contain three barcodes with spacers.
the command looks like that
```
$ bbduk.sh -Xmx100g in=10_ID_mRNA_S1_L002_R1_001.fastq
windows. However, I am not finding the way of doing that with the gene density. I have an annotation file with the genes and their coordinates, but how can I convert that to a file with number of genes in an specific sliding windows
Hi,
I am trying to do some differential expression experiments on my bacteria strain and I am very new to the field.
I aligned my (paired-end) reads with STAR to both a genome and plasmid (using 2 separate fasta files + 1 combined gff file, which was checked for identical annotation format). Afterwards I used featureCounts, but unfortunately, I couldn't detect some of the essential genes of the…
updated 2 days ago • heelpPlease
exome panel bed file (SeqCap EZ Exome v2, Roche, cat. no. 05860482001)
I came across this file in a paper I would like to utilize their analysis, however
I analyzed a protein-protein interaction analysis via CellPhoneDB package v5. The out put are these files:
1- Deconvoluted
2- Significant_means
3- Means
4- Pvalues
It sounds the significant means file is the important file. I am
updated 2 days ago • piotto
Hi, I am trying to run WGCNA analysis for wheat expression data. When I run `sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5)`, I get this as output file
```
Power SFT.R.sq
1) 0.915
2) 0.721
3) 0.179
4) 0.0866
5) 0.373
6) 0.523
7) 0.612
8) 0.674
9) 0.701
10) 0.726
12) 0.759
14) 0.808
16) 0.804
18...I run …
updated 2 days ago • deepak180001
Hello,
I tried to use vdjtools comvert clonotypes to vdj format.
It said: "[ERROR] java.lang.RuntimeException: Unable to parse clonotype string 4".
Thanks in advance for great help!
Best,
Yue
ThinkStation-P330:~/sph_data/vdjtools-1.2.1$ java -jar vdjtools-1.2.1.jar Convert -S MiXcr
36_clonotypes.TRA.tsv TRA.txt
WARNING: An illegal reflective access operation has o…
updated 3 days ago • yueli7
want to make a tissue-specific expression analysis using multiple tissues. I have lots of raw FastQ files that I retrieved from the ENCODE database. After successfully completing the alignment and quantification steps
protein_version "1";
I have a reference genome :
sequence.fasta
and a bam file :
ILS_W_V_558_S2_R1_001_val.bam
that looks like this :
samtools view ILS_W_V_558_S2_R1_001_val.bam | head
NB551648...XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:DP
I want to see gene specific coverage from the bam file.
result should look like
gene_name in 1st column and its Coverage in 2n…
updated 3 days ago • Adyasha
Cell In[8], line 1
----> 1 mod = cell2location.models.Cell2location.load(f"{run_name}", adata_ref)
File ~/miniconda3/envs/cell2loc_env/lib/python3.9/site-packages/scvi/model/base/_base_model.py:702, in BaseModelClass.load
updated 3 days ago • sidrah.maryam
to analyse genomic data and have encountered an issue where my VCF output (the sample_gam.vcf file) has no variants, despite expecting variants. I'm using VG version 1.52 on my HPC, in which I execute using Singularity.
Here...overview of the workflow I've run so far. Each generic filename in the commands represents an actual file:
-----------------Generate VG-------------------
si…
updated 3 days ago • sarumonsus
I am trying to go from the .map .lgen .fam to a ped file so that I can convert it to a vcf file since I am more used to working with those. However when I run
plink --lfile HeartData...I am trying to go from the .map .lgen .fam to a ped file so that I can convert it to a vcf file since I am more used to working with those. However when I run
plink --lfile HeartData --recode
I get th…
Hi everyone,
I have a vcf file from which I would like to retain (i) a list of known, associated SNPs and (ii) background, independent variants that are not...linkage with my associated SNPs one by one. For example, I could add associated variants to the vcf file, use vcftools to calculate r2 in the neighborhood around each associated variant, and form a list of associated background
updated 3 days ago • Jautis
I am new in this field. I am doing complete assembly from Illumina paired-end sequencing. I have nuclear sequencing .fastq (R1 and R2) files from which I mapped with mitochondria reference genome and extract the mitochondrial sequences and assemble with getorganelle and spades. i get the scaffolds and contigs files from both of them. Now i want to do gap closure and to make it circular genome. An…
updated 3 days ago • KHURRAM SHAHZAD
option (reference annotation) is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts" - my assumption was that it would somehow assist in the merging process of the individual...GTF's into the final non-redundant GTF. What I noticed though was that the resulting GTF file is much, much bigger in file size if that parameter is included. After som…
updated 4 days ago • DGTool
code
count <- Read10X("GSM4909254/") #give the name of the folder contains the mentioned files
srobj <- CreateAssayObject(counts = count, project = "GSM4909254",
min.cells = 3, min.features = 200) #filter the data
head(srobj
sci/labs/maayan.salton/adi8897/R_libs")
library(DESeq2)
# Define the full paths to your count files for the first analysis (Israeli_WBP4_mutant)
countFiles <- c(
"SRR9600556_sorted_counts.txt",
"SRR9600557_sorted_counts.txt...output_1024-3.counts" # Israeli_WBP4_mutant
)
# Sample names extracted from file names
sampleNames <- gsub("_sorted_counts.txt|_counts", "", countFiles)…
updated 4 days ago • adi.gershon1
lt;-intersect(colnames(mat),sig.gene70$HUGO.gene.symbol)
mat_filt<-mat[,genes_sign]
saveRDS(mat,file="x.rds")
saveRDS(mat_filt,file="x_filt.rds")
saveRDS(clinical$MP_risk,file="y.rds
Hi,
I have metadata containing information on 15 samples and a SNP-map file with columns: Index, SNPName, Chromosome, Position, GenTrain Score, SNP, ILMN Strand, Customer Strand, and NormID. Additionally...I have a file with allele information, including columns for SNP Name, Sample ID, Allele1 - Forward, Allele2 - Forward, Allele1 - Top, Allele2
updated 5 days ago • drajangirija
I'm currently working with gnomix and i need the GRCh38.gmap file. Could someone please direct me to where I can download it
DADA2 and Qiime2-amplicon-2023.9, I performed quality filtering using the following code:
```
for file in "${INPUT_DIR}"/*.fastq; do
base_name=$(basename "${file}" .fastq)
bbduk.sh in="${file}" out="${OUTPUT_DIR}/${base_name}.fastq" qtrim=rl trimq...10
echo "Processed file: ${file}"
done
```
Afterwards, I conducted a FastQC analysis, and the results looked promising. Initially, I en…
updated 5 days ago • Valentina
message:
"Aligner (--aligner) not specified. Did not find Bowtie/Bowtie2/BWA paths and/or index files
Please check: you have provided the full path to the aligner INCLUDING the executable filename
Please check: the specified...genome indices comprises the full path AND the basename of the index files
See documentation for further details"
And I already changed the path and uncomment the aligners …
updated 5 days ago • Ximena
Hi guys,
does anyone know how I get `TaxID mapping file` for NR or Uniprot database?
Background:
I use `Diamond` for my de novo transcriptome annotation. My next goal is to use hits...tsv file in `blobtools` for contamination detection. To do that **I need my query transcript IDs with the corresponding subject...in hits.tsv file. Diamond doesn't give that information but I can use `blob…
updated 5 days ago • Lada
from patients with pancreatic cancer cohorts from the ICGC. We only have access to the VCF files of the patients, from which I extracted the SNV and indel variants for each patient, filtering them to retain only the...to do this, WGS/WES data is required, which we don't have access to (we can't handle the BAM files due to memory issues). I considered using bcftools consensus to generate FASTA fil…
updated 5 days ago • Javier
then which allele is labelled as minor will depend on which was first encountered in the PED file.")
I am really hoping I dont have to extract those variants, convert to ped, then figure out which came first. Is there a better
updated 5 days ago • curious
me error as below. i have used featurecounts software for the same data and genome annotation file and the results are fine. since i need fpkm or rpkm values for normalization so featurecounts is not giving that output
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Did you get this figured out? I am having the same error in R.
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Try this:
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Answer: How to convert normalized BigWig file to count matrix?
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It's not possible. Gene counts are a region aggregate, bigwigs are a per-base readout and you cannot use normalized counts for mentioned to…
Comment: bcftools - reducing to "sites-only"?
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> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: bcftools - reducing to "sites-only"?
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Thank you Pierre!
Not sure why I didn't notice that (I should have)
Comment: How to convert normalized BigWig file to count matrix?
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bigwig is chrom/start/end/value . what kind of matrix do you want ?
Comment: How to convert normalized BigWig file to count matrix?
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I want to use the matrix derived from bigwig files to perform different analysis by DESeq2 or edgeR.
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> could you please explain what the collate does?
http://www.htslib.org/doc/samtools-collate.html
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Thank you for the feedback! I already used just the `samtools fastq -1 R1.fq.gz -2 R2.fq.gz -s Rx.fq.gz -0 R0.fq.gz`. Could you please exp…
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faster use samtools collate+ fastq
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