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Old 10-16-2015, 12:50 AM   #1
Rahul shelke
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Location: Guwahati,India

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Default SRA format, RNAseq, fastqc

Hello,

I have downloaded SRA data from NCBI and converted it into Fastq file (Pair end sequences), then i analysed the sequences using fastqc. The following results I got, which I think ok. But still confuse. Can anybody shade some light on this aspect. (Per base sequence quality http://dropcanvas.com/#aG53s1AtEBgLv1 )

##FastQC 0.11.2
>>Basic Statistics pass
#Measure Value
Filename PPlf.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 24000000
Sequences flagged as poor quality 0
Sequence length 75
%GC 44
Can I use fastq sequences derived from SRA format directly for assembly and scaffolding purpose ? or else i will have to do pre processing like removal of low quality reads,trimming of low quality bases,adapter removal?

regards

rahul
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Old 10-16-2015, 04:05 AM   #2
GenoMax
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You should pass these through a trim/filter program to be sure that there is no extraneous sequences in this dataset. Since you want to assemble the reads filtering some of the low quality bases may also be best.
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Old 10-16-2015, 04:48 AM   #3
Rahul shelke
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Thank you sir. usually whatever SRA file (Fastq) we download can we use them directly just by trimming /masking for assembling.

Regards
rahul
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