Question: how i can use SRA accession Number to call raw reads ?
gravatar for sh_shaddad77
12 months ago by
sh_shaddad770 wrote:

i have project to align 2 genome . Generated the reference index: bwa index reference.fa Then i want to align the reads to the reference index bwa mem reference.fa reads1.fq reads2.fq > aligned_pairs.sam To download the reads for the second genome , i use the genome deposit SRA accession number to download from ENA . the page present option : FASTQ files (FTP) NCBI SRA file (FTP file1 file1 file2 SRA accession number SRR1779159 which one should be used ?

alignment genome • 365 views
ADD COMMENTlink modified 11 months ago by yasokannan9320 • written 12 months ago by sh_shaddad770
gravatar for yasokannan93
11 months ago by
yasokannan9320 wrote:

Both the options (FASTQ files FTP and NCBI SRA file FTP) can be used. Its the same file.

ADD COMMENTlink written 11 months ago by yasokannan9320

Yep, should be all the same but you would need to convert the sra file to fastq which is additional effort. I always use FASTQ files (FTP), see Fast download of FASTQ files from the European Nucleotide Archive (ENA)

ADD REPLYlink modified 11 months ago • written 11 months ago by ATpoint36k
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