Questions tagged [filtering]

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RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias

I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters. Aim We would like to conduct SNP discovery of these samples. ...
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3 votes
2 answers
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How to subset a GRanges object based on a specific genomic window of interest?

Goal: To keep only rows of a GRanges object if their start coordinate is within 1 Mb of the start coordinate of a gene of interest. I am aware of some functions that come close: ...
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-2 votes
1 answer
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What are values of FILTER column of vcf files produced by Mutect2

I have called SNVs with Mutect2, now in filter column of a file called filtered vcf I have a lot of things like ...
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1 answer
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How to extract a subset of individuals from a .bgen file?

I have 10,000 controls and 3000 cases and the .bgen file has genotype of 200,000 individuals. I would like to extract only those individuals from the .bgen file that are either cases or controls using ...
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3 votes
3 answers
64 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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0 votes
2 answers
162 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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0 answers
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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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-1 votes
2 answers
91 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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1 answer
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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 ...
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2 votes
2 answers
152 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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1 vote
3 answers
72 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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0 votes
0 answers
502 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 ...
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1 vote
0 answers
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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 ...
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-1 votes
3 answers
116 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 ...
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1 vote
0 answers
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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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0 votes
2 answers
693 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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1 answer
126 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 ...
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1 vote
3 answers
512 views

Edit all the fasta headers using awk

kindly your comment highly appreciated have more than 4k header sequences look like: ...
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1 vote
1 answer
53 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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2 votes
0 answers
129 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? ...
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3 votes
1 answer
245 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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1 vote
0 answers
36 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
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3 votes
1 answer
392 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. ...
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2 votes
2 answers
840 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? ...
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6 votes
5 answers
2k 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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1 vote
0 answers
239 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 (...
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2 votes
1 answer
804 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: ...
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  • 617
3 votes
1 answer
209 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 ...
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5 votes
1 answer
534 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 ...
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5 votes
1 answer
509 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 ...
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11 votes
1 answer
2k 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 ...
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10 votes
6 answers
6k 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 ...
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1 vote
1 answer
238 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 ...
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  • 143
2 votes
3 answers
948 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 ...
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6 votes
4 answers
610 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 (<...
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7 votes
2 answers
3k 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 ...
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6 votes
2 answers
940 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 ...
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  • 5,287
9 votes
5 answers
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. ...
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