Questions tagged [filtering]

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1answer
13 views

How to copy only certain counts for genes in tsv file to new file in linux

Hi there I have generated a counts table of samples I need to compare by differential expression analysis. The layout of the counts table is as follows: Gene_id Sample_A_r1 Sample_A_r2 Sample_B_r1 ...
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2answers
50 views

Using grep to get lines from a file (.tsv) that contain specific samples listed in a sample file (.tsv)

So I have a file, let's call it pcawg.tsv. It's formatted like the one down below. ...
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0answers
24 views

Is there an easy way to identify nuclear genes using scanpy?

This question has also been asked on Biostars Scanpy has documentation where mitochondrial genes could be easily filtered out using ["MT"]. I was wondering if anybody has information on ...
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2answers
68 views

Filter rows of VCF file for Match=EXACT?

How do I remove rows in a VCF file on 1kGenome column, where Match=EXACT using bash ?
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1answer
32 views

Annotating gene names or gene IDs to a dataframe containing SNPs?

I have a large data-frame (excel file) of SNPs with genotyping data. I need to filter the data to get SNP information of a specific gene alone. The list is too long to do it manually. I was wondering ...
2
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2answers
99 views

How to remove sequences from a fasta file using a sequence ID list which contains a space within the id?

I have a fasta file that contains sequence reads and sequence id file that needed to be removed from the fasta file. I have done this earlier, but since id contains a space my piece of code is not ...
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3answers
54 views

How to filter out partially similar strings from two lists and make one list?

I have following two lists. List1 ...
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0answers
48 views

FMT/DP of missing genotypes in bcftools

I have a VCF file where the FMT/DP of missing genotypes has been recorded itself as missing data (".") When I filter ...
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0answers
211 views

Filtering samples by FORMAT attributes using bcftools

The -e and -i options of the bcftools filter command appear, by default, to only allow for ...
1
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0answers
23 views

Discard Candidates if N >= 40%

I have obtained ( interspersed repeats ) libraries in the Palm plant genome. Still, unfortunately, the candidates obtained seems false positive a lot of tandem repeats found, due to denovo ...
-1
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3answers
85 views

Discard sequences contain Ns

I have Fasta file contain multiple sequences, some of those sequences contain N's or n's, I'm trying to discard all the sequences and related header that contain Ns or ns in the file. I have tried ...
1
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0answers
28 views

Filtering pileup from site lists

I want to write a script that filters a pileup file from a site lists file. As an input I get a reference genome, pileup and site lists files. Example of an output for this script: Pileup File : ...
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2answers
390 views

Extract sequences from partial Header

I have a library I would like to split them based on their headers. Some are related to RNA and DNA. The header contains much information, but the most important the presence of DNA or RNA/LTR.., ...
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1answer
81 views

Filtering raw sequencing reads

I have to filter the raw sequencing reads based on the following criteria: Remove reads containing adapters Remove reads containing N > 10% (N represents base that could not be determined) Remove ...
1
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3answers
348 views

Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
1
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1answer
52 views

How do I create a filtered gene list using expression medians

Forgive the simple noob question I have TPM data of ~50k genes (rows) across ~1k cell lines (columns). In R, I would like to output an "intermediate expression" gene list for each cell line, like: <...
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0answers
110 views

Empty values in FILTER field after running Mutect2

I was expecting something like in this image: But when I ran Mutect2, the FILTER field was empty in the output VCF file. How can I enable PASS filters? ...
3
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1answer
215 views

Fast processing of fastq data

I am trying to write python script for customized filtering for fastq file (size >3 GB). My proposed script is as follows: ...
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0answers
35 views

ExpressionSet with a custom gene list

After an ExpressionSet is established, I want it to contain only the genes of my choice ("selected.txt") What is the best approach?? Thanks
3
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1answer
337 views

Output from vcftools missingness

I'm new to data filtering on vcf data and vcftools. I performed variant calling on my dataset, CHR22, homo sapiens. I'd like to remove sites that are missing in more than 5% of individuals. ...
2
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2answers
697 views

How can I extract the longest N isoforms per gene from a fasta file?

The question of how one can extract the longest isoform per gene from a multi-fasta file has been answered expertly in this thread: How can longest isoforms (per gene) be extracted from a FASTA file? ...
6
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5answers
1k views

Delete all 4 lines of a fastq read from a fastq file using read ID

I have the following error when running bowtie2: Error: Read HWI-D00466:116:CC62WANXX:3:1102:7363:63646 1:N:0:GCACACG has more read characters than quality values. I now want to remove all 4 ...
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0answers
227 views

Error filtering SNPs with Plink

Im trying to filter SNPs using PLINK with this command. Also, the .map and .ped files were converted to a plink format from a vcf file (...
2
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1answer
590 views

Select top 100 genes ranked by variance in read counts

I have a gene expression data (read counts) table with many samples. Showing some of them below: ...
3
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1answer
187 views

How to filter Ensembl cDNA and ncRNA FASTA files by primary assembly?

I'm currently performing differential expression analysis using alignment-free quantification using Kallisto. To do this, I need to create a Kallisto index using Ensembl's cDNA and ncRNA annotations ...
5
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1answer
488 views

Single-cell RNA sequencing (scRNA-seq): filtering cells by transcript counts, how to choose cutoffs?

I am running a notebook with example for the MAGIC algorithm. In the data preprocessing step, a filtering operation is required to filter out cells with a small count of transcripts. My question is ...
5
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1answer
413 views

Filter out outliers of the scRNA-seq (heterogenous cells)

I am new to data science. I have a dataset of single-cell gene expression from multiple cell types in C. Elegans. The dataset is from the paper Comprehensive single-cell transcriptional profiling of a ...
11
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1answer
1k views

Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter?

Disclaimer: This is a self answered question for documentation purpose and I adapted this from the following github gist. Especially from users terrycojones and peterjc as well as sujaikumar who ...
9
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6answers
5k views

How do I find identical sequences in a FASTA file?

I want to create a database for a proteomics study. Therefore, the mapping from a given sequence to a protein ID has to be unique. I am wondering whether there is already a built-in function in ...
1
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1answer
232 views

Filtering out all seqs with mutations of list2 from list1

I have 2 lists, list1 and list2, of protein sequences of the same given gene in different strains. In ...
2
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3answers
870 views

Filter BAM file for read pairs where one or both of the reads starts with a given sequence pattern

What's the most straightforward way to filter a BAM file for read pairs where one or both of the reads starts with a given sequence pattern? Would a tool that deals with UMIs work for this? Which one ...
6
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4answers
490 views

Any fast options to query large VCF bed intervals?

I'm doing some analysis and I need to subset a large VCF file (~8GB gziped) given a bed interval and identify within a subset of rsid. Unfortunately, both my normal choices to do this analysis (<...
7
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2answers
2k views

Filtering step for read counts data

I have around 1200 samples as columns and 60,000 genes with Htseq-Counts data. Before normalization with voom function I want to do filtering step. I want to remove genes whose expression is == 0 in ...
6
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2answers
816 views

How to safely and efficiently convert subset of bam to fastq?

Question How can I extract reads from a bam file (produced by bwa-mem) to fastq given a ...
9
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5answers
3k views

How can longest isoforms (per gene) be extracted from a FASTA file?

Is there a convenient way to extract the longest isoforms from a transcriptome fasta file? I had found some scripts on biostars but none are functional and I'm having difficulty getting them to work. ...