paired end reads don't have the same length

[fnn4]

Dear all,

My genomes were sequenced by illumina hiseq in paired end. I was running cortex but it died in SAM line1 says the list of paired end reads don't have the same length and quit. How should I process it?

Thank you!

[Brian Bushnell]

You should re-obtain the raw read files that have the correct number of reads, and start with those. Then, you'll have to clarify what you are trying to do next.

[fnn4]

You should re-obtain the raw read files that have the correct number of reads, and start with those. Then, you'll have to clarify what you are trying to do next.

Thank you for replying!
I'm using files of raw reads though. How can I make them the same length?
Thank you!!

[Brian Bushnell]

Can you post the head, tail, and wordcounts of the two files?

e.g. the output of these commands:

head -n 8 read1.fastq
tail -n 8 read1.fastq
wc read1.fastq

head -n 8 read2.fastq
tail -n 8 read2.fastq
wc read2.fastq

[GenoMax]

Brian: Sounds like some of the reads are not the same length (total number may be the same). Perhaps "cortex" (not sure what that is) requires them to be.

[fnn4]

The files sizes are the same when they are in fastq, but not the same when they are gziped. But even when I use fastq files, it still quit saying paired end reads don't have the same length, die SAM line 2.
below is one's sample's head, tail wc.
head -n 8 E_F.fastq
@HWI-ST1360:45:C1JK9ACXX:1:1101:3383:2427 1:N:0:TGACCA
TCAATTCGACTGGGTACGACCACGTAAGACATGGTTAGATGCAAAATGTCCAGTGTATATTGATTTTGGTGACGAACACCTTGTAAAACTAGATACATATG
+
BBBFFFFFFFFFFIFFIIIIIIIIFIIIIIIIIIFIIIIIIIIIIIIIFIIFIFFFFIIIIIIIIIIFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFF
@HWI-ST1360:45:C1JK9ACXX:1:1101:3303:2477 1:N:0:TGACCA
AGAGATAACCAACAGTTCGCGTTTGAATATCAAGACAATGAAGGCCAAACACAATCTAAAGCATTAACACTCAAAGTAGGCGATAGCCTTGAAGAAGTGGC
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB

tail -n 8 E_F.fastq
@HWI-ST1360:45:C1JK9ACXX:1:2316:20760:100871 1:N:0:GGACCA
TGTCATATCCGCAAAGCTCTGAAATGACATTATTTTCAATAGCCTCAACGGCTAATTGGTTGGCGCGGGCAGTATTGATACAAATACGATGCCCTTGCTCG
+
BB<FFFFFFFFFFBFFIIFFFFFFIIFIFFFFFFIB<FBFFFFIFFBBFFFF<FBFFFIIIIFBBBFFBB<<'0<BBFFFFBBBBBFB<BFBBBBBB<BBF
@HWI-ST1360:45:C1JK9ACXX:1:2316:21212:100876 1:N:0:TGACCA
TTTTCTAAAGCGATACAACCTTACAGGTAAACTGGAAGCCGGTTTGTATCACTTGTCCGTTGTATCTAAAGATAAACAAGTTTACAGAACTTGGGTGATAC
+
7<B<B<00<B0<<BFFFB00<BFBBB'0<0BF<07BFB0'<77BF<7BB'<BBBB70<7BBFBBFBB<BB<BBBBBB<<B<<<<7'0<<<''070077<<'

wc E_F.fastq
16531308 20664135 1084831013 E_F.fastq
wc E_R.fastq
16531308 20664135 1084831013 E_R.fastq

Thank you!!

Can you post the head, tail, and wordcounts of the two files?

e.g. the output of these commands:

head -n 8 read1.fastq
tail -n 8 read1.fastq
wc read1.fastq

head -n 8 read2.fastq
tail -n 8 read2.fastq
wc read2.fastq

[Brian Bushnell]

The fact that both files have the exact same number of lines and characters indicates that probably there is no problem with the input, but rather some kind of bug in cortex (which I have also never heard of) or an incorrect command line.

What are you trying to do with the data?