Questions tagged [filtering]

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return cds from a protein fasta based on gene ID in unix?

I'm trying to retrieve cds sequences for given genes. Which requires taking a list of genes gene27 gene28 Retrieving their Gene ID (LOC##) and using faa to ...
3
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1answer
137 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
32 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
80 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
108 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
236 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
130 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
53 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
76 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
286 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
159 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 ...
9
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1answer
701 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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5answers
2k 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
216 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
557 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
254 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
872 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
446 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
1k 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. ...