Hi all, I am a bit new to assembling stuff. Please spare me and answers even if my questions looks a bit silly.
I obtained an .SRA file ( 200bp PE Illumina reads ) from NCBI traces archive. Using sratoolkit it is converted to fastq format.
(fastq) It looks like this:
@SRR018008.1 307AEAAXX:4:1:1591:659 length=84
GATTTTGAAGGCATATCTTGAAGATGGTGCAGCATCCGAGGTAAGAGACGGGTGAAGCATGGAGCAGAGCGTCAGCAGATGGTG
+SRR018008.1 307AEAAXX:4:1:1591:659 length=84
IIIIIIIIIIIIIIIIIIII?=IIII;IGBI,<:I8:2/5+8IIIIIIIIIIIIIIII:?ID,ID3I1<8C,4:6-.5-+)3(9
@SRR018008.2 307AEAAXX:4:1:1593:693 length=84
GAATTGGCAATCGTCCAATCGTCCAAACGTCCAGAGAGCCGCATAATTACCCGTCACGAATTTCTCTGCTTTGCAGCCGAGCAA
+SRR018008.2 307AEAAXX:4:1:1593:693 length=84
IIIIIIIIIIIIIIIII;II-III0//IH0/;3726,9&5/57IIIIIIIIII,IIIIIBI8A>?)II:AI56;1910056$(%
@SRR018008.3 307AEAAXX:4:1:1672:656 length=84
GGTAGACTTAGTGAATGAACGAAGGGTATCAAAAGATGGAGTCTGCCACCGGCTCGCTGCTCACATCGGAGACCAGCCTGAGCA
+SRR018008.3 307AEAAXX:4:1:1672:656 length=84
IIIIIIIIIIIIIIIIIIEII==IIIH?IIE25-I:G=+5/,IIIIIIIIIIBHI/I490B447-,0-6)90*-%+(('+%*'&
Now my questions are:
1.After conversion SRA-> fastq i obtained only 1 file with read length =84 as shown above. Is it a Single End read (SE) file? If so how can i convert a paired end (PE) file?
2. Is the length=84 present in the file is obtained due to trimming of the ends 100-(8+8) ? if not what does length=84 means?
3. This is bit unrelated to above content:
what is the difference between
a)./velveth sillyDirectory 21 -short data/test_reads.fa
b)./velveth sillyDirectory 21 -short data/test_reads.fa -long data/test_long.fa
Please kindly help me understanding basic concepts. Would be grateful to your answer.
I obtained an .SRA file ( 200bp PE Illumina reads ) from NCBI traces archive. Using sratoolkit it is converted to fastq format.
(fastq) It looks like this:
@SRR018008.1 307AEAAXX:4:1:1591:659 length=84
GATTTTGAAGGCATATCTTGAAGATGGTGCAGCATCCGAGGTAAGAGACGGGTGAAGCATGGAGCAGAGCGTCAGCAGATGGTG
+SRR018008.1 307AEAAXX:4:1:1591:659 length=84
IIIIIIIIIIIIIIIIIIII?=IIII;IGBI,<:I8:2/5+8IIIIIIIIIIIIIIII:?ID,ID3I1<8C,4:6-.5-+)3(9
@SRR018008.2 307AEAAXX:4:1:1593:693 length=84
GAATTGGCAATCGTCCAATCGTCCAAACGTCCAGAGAGCCGCATAATTACCCGTCACGAATTTCTCTGCTTTGCAGCCGAGCAA
+SRR018008.2 307AEAAXX:4:1:1593:693 length=84
IIIIIIIIIIIIIIIII;II-III0//IH0/;3726,9&5/57IIIIIIIIII,IIIIIBI8A>?)II:AI56;1910056$(%
@SRR018008.3 307AEAAXX:4:1:1672:656 length=84
GGTAGACTTAGTGAATGAACGAAGGGTATCAAAAGATGGAGTCTGCCACCGGCTCGCTGCTCACATCGGAGACCAGCCTGAGCA
+SRR018008.3 307AEAAXX:4:1:1672:656 length=84
IIIIIIIIIIIIIIIIIIEII==IIIH?IIE25-I:G=+5/,IIIIIIIIIIBHI/I490B447-,0-6)90*-%+(('+%*'&
Now my questions are:
1.After conversion SRA-> fastq i obtained only 1 file with read length =84 as shown above. Is it a Single End read (SE) file? If so how can i convert a paired end (PE) file?
2. Is the length=84 present in the file is obtained due to trimming of the ends 100-(8+8) ? if not what does length=84 means?
3. This is bit unrelated to above content:
what is the difference between
a)./velveth sillyDirectory 21 -short data/test_reads.fa
b)./velveth sillyDirectory 21 -short data/test_reads.fa -long data/test_long.fa
Please kindly help me understanding basic concepts. Would be grateful to your answer.
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