Dear all,
I have large fastq files (about 6-7 Gb each of them), which their headers are not compatible with trinity program as the following error appeared after running trinity:
Error, pairs.K25.stats is empty. Be sure to check your fastq reads and ensure that the read names are identical except for the /1 or /2 designation
My header left fastq file is:
@D69F08P1:337:C4GGBACXX:2:1101:1378:2161 1:N:0:ATGTCA
GGGGGCAGTGACCAGCTGGACTGAGCTCATAGTATGGAGCTTCAGGCAGCTGCCTTTTCACCTGAAGGCCCCAGATAGGCTTAACCCAGGGGTCTTCTTT
+
BBBFFFFFF<FFFIIIIIIIIIIIIIIIIIIIBFFIIIFIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFF77BBFFFF
@D69F08P1:337:C4GGBACXX:2:1101:1497:2202 1:N:0:ATGTCA
TATGGATGGTGATCACTCAGGCTGAAACCCCCAGCAAGGAATCTTTGGATGAGGGCCAGCTGAGATCTCTCTTGGTCGGAGTATGCATCCATGATCATGG
and the right fastq file header as
D69F08P1:337:C4GGBACXX:2:1101:1378:2161 2:N:0:ATGTCA
GTTCCAATCTGTCTCATGTATGGAAAAGAAGACCCCTGGGTTAAGCCTATCTGGGGCCTTCAGGTGAAAAGGCAGCTGCCTGAAGCTCCATACTATGAGC
+
BBBFFFFFFFFFFIIIIIFIIIIIIIIFFIIIIIIIIIIIFIIIIFIIIIIIIIIIIIIIIIIIFFIIFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFF
@D69F08P1:337:C4GGBACXX:2:1101:1497:2202 2:N:0:ATGTCA
CGAATATAGAGAAAGCCAGCAGACTTGCCAATGTGCCTTCTGGGATGAAGACAATTCCGACGACTTAGTCTCCCAATCTGCCCAGGAATCAGATCAATGG
I think the header (say left reads) should change to @D69F08P1:337:C4GGBACXX:2:1101:1378:2161:N:0:ATGTCA/1 that is acceptable for trinity, am I right?. Could you please share your commands to this end? Thanks so much in advance
To convert (though not parallelised):
awk '{ if (NR%4==1) { print $1"_"$2"/1" } else { print } }' Read1.fastq | less
awk '{ if (NR%4==1) { print $1"_"$2"/2" } else { print } }' Read2.fastq | less
But you can read this thread from trinity google group.
To save to file:
awk '{ if (NR%4==1) { print $1"_"$2"/1" } else { print } }' Read1.fastq > rename_Read1.fastq
awk '{ if (NR%4==1) { print $1"_"$2"/2" } else { print } }' Read2.fastq > rename_Read2.fastq
Thanks a lot Geek. It works fine with unzip files, but I didn't know why it doesn't work with gzip file, even I applied "gunzip filename | " before your command! I'm dealing with many large files, any suggested command to solve the problem would be really appreciated.
Did you read the Google thread ? I have used trinity recently on raw fastq from illumina HiSeq1000 and it worked fine without any error regarding /1 or /2. Regarding gz files, use
zcat filename | command | gzip > out.gz
•
written
by
GouthamAtla
Are you sure the problem are fastq headers? I have used recent versions of Trinity (versions r20140717 and 2.0.6) with files with the same kind of headers you have, and did not have problems. Did you pre-process your files with some software ignoring read pairs? To quickly test if your files have uneven number of lines (hence reads are unpaired), do:
zcat Read1.fastq.gz | wc -l -
zcat Read2.fastq.gz | wc -l -
Yeah. If you have done any preprocessing, the reads should be reordered. Otherwise they lose pairing information.
I have single end reads, so just needed to add a '/1' to my IDs that were generated by the samtools bam2fq command.
sed gets confused adding the '/' (forward slash) character to a file.
I did it with:
awk '/^@HISEQ/ {$0=$0"/1"} 1' original.fq > newfile.fq
This command looks for likes beginning in '@HISEQ' and adds a '/1' to the end of that line.
For example:
original fastq header
@HISEQ-MFG:77:HFTM7BCXX:1:1101:1436:2041
CCGCATTCCAAACGGGGCCTA
+
DDDB@EHHHHHIIHIIIHHII
same header after awk '/^@HISEQ/ {$0=$0"/1"} 1' bam2fq.fq > newfile.fq
@HISEQ-MFG:77:HFTM7BCXX:1:1101:1436:2041/1
CCGCATTCCAAACGGGGCCTA
+
DDDB@EHHHHHIIHIIIHHII
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