A function to extract pair end reads from the bam file generated with subread functionRaffaele A Calogero
Eg a slice covering a large region followed by a slice with just a few bases, due to an overwhelming depth of short soft-clipped reads. In some cases, this could then trigger reading uninitialised memory and using data from that for the second "end" file offset. So it may be fast, or...
Raw nanopore reads are processed by a single command to produce basecalls (FASTA/Q), reference mappings (SAM/BAM/CRAM), modified base calls (per-read and bedgraph/bedmethyl/modVCF), sequence variant calls (per-read and VCF) and more. ...
If you want to extract the sequences of for specific reads from the FASTQ file, based on their read IDs, you should generate an ids.txt file. This file should list the read IDs, with each ID on a separate line, as demonstrated below:cat ids.txt SRR22309490.1 SRR22309490.5 ...
This module provides functions to extract useful metrics from Oxford Nanopore sequencing reads and alignments. FUNCTIONS Data can be presented in the following formats, using the following functions: A sorted bam fileprocess_bam(bamfile, threads) ...
ByteFile.FORCE_MODE_BF2=oldBF2; FASTQ.TEST_INTERLEAVED=oldTestInterleaved; FASTQ.FORCE_INTERLEAVED=oldForceInterleaved; } public static void printOptions(){ Expand Down 39 changes: 23 additions & 16 deletions 39 current/jgi/ReformatReads.java Show comments View file Delete file This file cont...
Assuming your Hi-C reads are interleaved, with BWA MEM we recommend users ignore mate-pairing steps (-SP) and importantly require 5-prime alignments are primary (-5). bwa mem -5SP contigs.fasta.gz hic_paired.fastq.gz | \ samtools view -bS - > hic2ctg_unsorted.bam 3. Sort the ...
Samtools (v1.11) [59] was used to examine the mapped files, and raw read values for all of the annotated genes were determined using bedtools multiBamCov v2.30.0 [60]. Non-informative data were removed by filtering the genes with a total expression level less than 20 reads. To execute...
Addition of Glycyrrhiza uralensis (HEGU) to Drinking Water Inhibits Solid Tumor Growth and C2D.e1le.lcAPrerdaodsleiitfseioCrnaetloilofPnGraolynlicdfyertrharhteiioEznaxpaunrreadslsetihnoesniEsox(fHpPrEreosGsteiUoinn)stooRf DPelraroitnteedkiintnosgRAWenlaagttieeordgIetnnoheAsibinsitgasinoSgdoelIn...
while the rest two for longer sequences ranged from 70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the support of long reads and chimeric alignment, but BWA-MEM, which is the latest, is generally recommended as it is faster and more accurate. BWA-MEM also...