Hi SRA team, I have a question of how to check the integrity of the BAM or FASTQ files. The .sra.vdbcache files were downloaded using prefetch and validated using vdb-validate. But how can I check whether the extraction of BAM or FASTQ files from .vdbcache was complete and did not ...
fastq ids.txt > seq_subset.fastq Where, input.fasta or input.fastq are the name of your input FASTA/FASTQ files, and ids.txt contains the list of sequences IDs (one ID per line) to extract from the FASTA/FASTQ files.The ids.txt can also contains the sequence ID and specific sequence...
9.3 Convert SRA data into fastq files & compress them for srr in $(cat SRR_Acc_List.txt); do cd $srr; sratoolkit.2.11.2-ubuntu64/bin/fasterq-dump *.sra -e 8 --ngc prj.ngc; gzip *fastq; cd ..; done >& out_conversion.txt & This command will generate two fastq files if the...
23-2 R2013a Saving to FASTQ, FASTA, SAM, and BAM files from a BioMap object . . . 24-2 Sorting unordered BAM files using BioMap objects . . . . . . . . . . . . . . . . . 24-2 Visualize and explore quality statistics of unmapped short-read data using BioRead and BioRead...
hisat2 -p 20 -x index/chi_masked -1 rna-seq/leaf_ox_r1_1.fastq.gz -2 rna-seq/leaf_ox_r1_2.fastq.gz|samtoolssort-@ 10>02-barker/leaf_ox_r1.bam&isat2 -p 20 -x index/chi_masked -1 rna-seq/ox_flower9_rep1_1.fastq.gz -2 rna-seq/ox_flower9_rep1_2.fastq.gz|samtools...