Question: how i can use SRA accession Number to call raw reads ?
gravatar for sh_shaddad77
5 weeks 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 • 168 views
ADD COMMENTlink modified 5 weeks ago by yasokannan9320 • written 5 weeks ago by sh_shaddad770
gravatar for yasokannan93
5 weeks 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 5 weeks 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 4 weeks ago • written 4 weeks ago by ATpoint23k
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