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Old 02-10-2011, 06:02 AM   #1
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Location: germany

Join Date: Mar 2010
Posts: 3
Default fastq-dump and paired end reads

Already solved - sorry for the post.

I downloaded all runs from a paired 50-nt reads experiment from SRA (SRP002274). When I use fastq-dump to generate fastq files (e.g. fastq-dump -A SRR039628 -D SRR039628.sra) everything works fine except that I only get a single file and not two pair files. It is not clear to me how I can identify read pairs from a single file since the read names only provide information about lane, tile, x and y but not "read pair number" (e.g. @SRR039628.1 HWI-EAS220_1_FC304WC_GEX:3:1:1056:45).
I am probably missing something obvious so any help is much appreciated.

Last edited by moritz; 02-10-2011 at 06:17 AM. Reason: Already solved - sorry for the post.
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Old 02-10-2011, 06:17 AM   #2
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I think I found the corresponding read (same spot) in another file. Sorry for the post.
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Old 09-11-2012, 03:45 AM   #3
Mamoon Rashid
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Location: KSA

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Posts: 8
Default dumping paired-end reads from .sra files

Dear All,
I am sharing an experience how to dump .sra file into fastq files. Always pass
flag to fastq-dump command. It will save forward and reverse reads in separate files. If the .sra file contains only the single end read only one fastq file will be generated.
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Old 01-09-2014, 01:57 AM   #4
Location: india

Join Date: Jan 2014
Posts: 11
Default query

kindly someone pls help me as to will the --split3 flag in fastq dump will surely generate a R1 and R2 file... as to I am not quite sure that my data is single ended or paired. when i converted using this flag and used for bowtie the result was as follows:
102886046 reads; of these:
102886046 (100.00%) were paired; of these:
95447806 (92.77%) aligned concordantly 0 times
3451944 (3.36%) aligned concordantly exactly 1 time
3986296 (3.87%) aligned concordantly >1 times
95447806 pairs aligned concordantly 0 times; of these:
30023949 (31.46%) aligned discordantly 1 time
65423857 pairs aligned 0 times concordantly or discordantly; of these:
130847714 mates make up the pairs; of these:
57243419 (43.75%) aligned 0 times
46040125 (35.19%) aligned exactly 1 time
27564170 (21.07%) aligned >1 times
72.18% overall alignment rate

I think this is not a good result for a paired seq.!!!

kindly help.
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read pairs, rna-seq, sra

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