How to download an SRA file containing alignment information from public repository

[srikant_verma]

Hi All,
I am trying to get an SRA file which contains alignment information. I want to use sam-dump to get the relevant sam/bam file.
I am able to download SRA file containing read information from NCBI SRA and can use fastq-dump to get back original fastq file. But not able to find a single SRA which has alignment information.
Can anyone suggest me how to do that?
Thanks

[dpryan]

I've never actually seen an SRA file with alignment information. While I'm sure they exist they're not exactly common.

[srikant_verma]

Yes... Ryan
I have been searching for last two days... have not found any.

[GenoMax]

@Srikant: So what is your aim? Try sam-dump program on real data?

Try your luck with this set:

http://sra.dnanexus.com/?result_type=Study&show=&q=with+alignments

[srikant_verma]

@GenoMax: Thanks for your input.
I downloaded two sra files (ERR409719.sra, ERR409720.sra) from the link given by you.
I ran the following commands:
$ vdb-dump ERR409719.sra > ERR409719_vdb_dump.out
$ vdb-dump ERR409720.sra > ERR409720_vdb_dump.out
$ cat ERR409719_vdb_dump.out |grep -E -e "ALIGNMENT_COUNT"
$ cat ERR409720_vdb_dump.out |grep -E -e "ALIGNMENT_COUNT"

I got no "ALIGNMENT_COUNT". It means these SRA files do not contain alignment information (as suggested by https://www.biostars.org/p/92747/).

Furthermore, I ran the following:
$ sam-dump ERR409719.sra |head
$ HWI-M01145:42:000000000-A3EYY:1:1101:17605:1446 77 * 0 0 * * 0 0 NCCTGATTGGTTCCGCACTGGCAAAACCTCTGACCGACTGGAAATGTAAAGTCACTATCTTCTGGTGGACGAACGCCCTGCTGGNNNNNATTAGCCTCGC #>>ABBFFFFFCGGGGGGGGGGHHHHHGHHHHHHHGGGGGHGHHHHGHHHHHHHHFHHHHHHHHHHFGFHGGGGGGGGGHHHHH#####???FFHHHHGG
HWI-M01145:42:000000000-A3EYY:1:1101:17605:1446 141 * 0 0 * * 0 0 ATCACGAAGATGAAGACAAACATAGTGATGCTNNNNNNCATGGGAACAAANNNNNNCGCGAGGCTAATCACTGCCAGCAGGGCGTTCGTCCACCAGAAGA B?ABBB@BBBFFGGGGGGGGGGHHHHHGHHHG######AABFGHHHGHFF######BBBFFGGEGHHGHHHHHGHGHGHHHGGGFGGGGGGEFGHHGHHH

It seems its a READ file.
So I ran:
$ fastq-dump ERR409719.sra
$ head ERR409719.fastq
$ @ERR409719.1 HWI-M01145:42:000000000-A3EYY:1:1101:17605:1446 length=200
NCCTGATTGGTTCCGCACTGGCAAAACCTCTGACCGACTGGAAATGTAAAGTCACTATCTTCTGGTGGACGAACGCCCTGCTGGNNNNNATTAGCCTCGCATCACGAAGATGAAGACAAACATAGTGATGCTNNNNNNCATGGGAACAAANNNNNNCGCGAGGCTAATCACTGCCAGCAGGGCGTTCGTCCACCAGAAGA
+ERR409719.1 HWI-M01145:42:000000000-A3EYY:1:1101:17605:1446 length=200
#>>ABBFFFFFCGGGGGGGGGGHHHHHGHHHHHHHGGGGGHGHHHHGHHHHHHHHFHHHHHHHHHHFGFHGGGGGGGGGHHHHH#####???FFHHHHGGB?ABBB@BBBFFGGGGGGGGGGHHHHHGHHHG######AABFGHHHGHFF######BBBFFGGEGHHGHHHHHGHGHGHHHGGGFGGGGGGEFGHHGHHH

Conclusion: These files are not alignment files.

Please suggest if I have missed any point.