Hey guys, first post (and thus a novice).
I've used TopHat before on my labs own data and it worked pretty well. Now I am using a data set from another lab and there is an issue. Nothing (except for ~2100 reads) maps to the genome.
BLASTing some of the sequences proves it's Drosophila RNA in the fastq file. I've provided a bit from the fastq, and my command line input. But if there is more you need then let me know.
I have a suspicion that it may be a problem with the formatting of the quality scores, having --solexa1.3-quals instead throws an error at the prep-read stage
Thanks guys.
.fastq sample:
@SRR070266.18 HWUSI-EAS1720_3:3:1:0:442 length=216
NGCCAAGCAAGGCGAATTTATTTATGCCACTAAGCGTGGTATTGTCCGACTACGGAATGACCATGAGATTACACTGGAGGATGTACTCTTTTGTAAGGAAGCTGCTGGCTTTTGTCAANNTCNATCGANANTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGG
+SRR070266.18 HWUSI-EAS1720_3:3:1:0:442 length=216
!(*)(-/,,'8::88FFFF;-5//3FF;FFFFFFF555-544333F;F5FF=;FF#####################################################5=@CC8B###!!##!#####!#!#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!###
Command line:
tophat -i 40 -p 5 -G ./GFF/dmel-all-r5.53.gff -o ./out/ --solexa-quals ./Dmel_AllChr_Bowtie2indx ./Testis-RNA-seq-ModEncode.fastq
I've used TopHat before on my labs own data and it worked pretty well. Now I am using a data set from another lab and there is an issue. Nothing (except for ~2100 reads) maps to the genome.
BLASTing some of the sequences proves it's Drosophila RNA in the fastq file. I've provided a bit from the fastq, and my command line input. But if there is more you need then let me know.
I have a suspicion that it may be a problem with the formatting of the quality scores, having --solexa1.3-quals instead throws an error at the prep-read stage
Thanks guys.
.fastq sample:
@SRR070266.18 HWUSI-EAS1720_3:3:1:0:442 length=216
NGCCAAGCAAGGCGAATTTATTTATGCCACTAAGCGTGGTATTGTCCGACTACGGAATGACCATGAGATTACACTGGAGGATGTACTCTTTTGTAAGGAAGCTGCTGGCTTTTGTCAANNTCNATCGANANTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGG
+SRR070266.18 HWUSI-EAS1720_3:3:1:0:442 length=216
!(*)(-/,,'8::88FFFF;-5//3FF;FFFFFFF555-544333F;F5FF=;FF#####################################################5=@CC8B###!!##!#####!#!#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!###
Command line:
tophat -i 40 -p 5 -G ./GFF/dmel-all-r5.53.gff -o ./out/ --solexa-quals ./Dmel_AllChr_Bowtie2indx ./Testis-RNA-seq-ModEncode.fastq
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