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Questions tagged [read-mapping]

When dealing with associating sequencing reads to a matching position in a set of reference sequences (typically a genome).

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Patient-sample mapping in GSE72056 dataset

I want to use the single-cell data from the following expression profiling which concerns the RNA-seq of metastatic melanoma: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72056 The data was ...
hadi's user avatar
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Converting EntrezGene IDs to Ensemble IDs

I am trying to convert my gene_id accessions given by the RNAseq as EntrezGene gene numbers into Ensemble annotation. I need the Ensemble annotation for further GO analysis. I am using BiomaRT package ...
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MAGs transcriptomics pipeline question

I have currently a following problem. I have a one sample that I did my metagenomics on (Illumina shotgun + nanopore) and have recovered some high quality MAGs. I also did a metatranscriptomics on the ...
Avamys's user avatar
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Merging/concatenating index files

I was wondering if any one has had success merging pre-generated reference index files for BWA, bowtie2 from multiple references? For a concrete example I have hg19 and a bunch of viral and ...
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How snippy makes MSA-like aligned fasta output from multiple samples?

From the log file it seems snippy doesn't do assembly. It only does mapping: fastq --> SAM --> BAM --> VCF --> consensus_seq/snps But if multiple ...
Ahmed Abdullah's user avatar
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Calculating alignment/mapping time

I am trying to assemble a plant genome using AWS resources using velvet. Plant genome is huge (> 10 times human genome) and coverage is around 30 x. We are planning for de novo assembly with Velvet (...
ssv's user avatar
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Visual representation of detecting deletion by different read types

I'm having some trouble differentiating between CNV, split reads and read pairs and how each one elucidates the presence of a structural variation, say deletion. Given a reference and donor sequence,...
Dianne's user avatar
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Is it normal to have low mapping to bacterial genome in a total RNA sample of plant root-colonized bacterial cells?

I had isolated the total RNA from a sample of plant roots with colonized bacteria by excising the roots (harboring the bacterial cells) and crushing them into a powder using liquid nitrogen. The RNA ...
K_081's user avatar
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Mapping statistics from the bam files

I would like to find the mapping statistics from the sorted bam files. Samtools flagstat gives the output only for a single file. What is the easiest way to find the mapping statistics for all ...
Kam's user avatar
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using Bowtie to map miRNA-seq data to rfam and also reference genome

I am using Bowtie to remove non-coding RNAs (tRNA, snRNA, rRNA) by rfam and also maping our microRNA-seq data with mirbase using following code: ...
user12371's user avatar
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How to rename Read Groups

I periodically run into problems with Read Groups. I am in a desperate need for a tool that would allow me to fix them. This time, when I was mapping reads, I formatted all the information in the Read ...
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How to choose reference to calculate coverage of WGS of organism that has high intra-species variation?

Calculation of coverage involves mapping reads with a reference and depending on the choice of reference we can get very different result. If a species has a genome that has very low size variation ...
Ahmed Abdullah's user avatar
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1 answer
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Mapping List of Probes/Primers/Short Oligos to a Reference Fasta/q

Could you help me bioinformatics SE people. So I have been duckduckgo-ing up a storm and even consulted the AI overlords and haven't come up with a solid way to do this, but it is so fundamental to ...
RPINerd's user avatar
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How to control/normalize for number of reads when calling SNPs using RNA-Seq?

I used the GATK pipeline to call SNPs on males and females using RNA-Seq data. But the males have a higher read count (~43-46M reads) than the females (~40-42M reads). This causes SNP counts to be ...
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How to obtain the extended unaligned bases of the read in reference based genome assembly?

I did illumina read mapping based on a particular gene sequence (reference sequence) using the following command, ...
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