Removal of non quality read in fastq file
I am trying to remove the non quality reads in fastq,
For Example
@NB501309:173:HYW77BGX5:1:11101:23920:1057 1:N:0:CATTTTAT+GGGGGGGG
TCTCANGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGGAAGT
+
AAAAA#EEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEAEEEA<EEE/AE<EEEEEEEE6EEEEEEEEEEAEEEEE
**@NB501309:173:HYW77BGX5:1:11101:19977:1057 1:N:0:CATTTTAT+GGGGGGGG
CCCGTNGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGAAAAA
+**
@NB501309:173:HYW77BGX5:1:11101:16270:1057 1:N:0:CATTTTAT+GGGGGGGG
ATTCTNGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGGGGGG
+
AAAAA#EEEEEEEEEEEEEEEEEEEEEEE/EEEEEE///AE//EE/EA/A/A//E//A<//EEEAEE///A/EEE
**@NB501309:173:HYW77BGX5:1:11101:15947:1058 1:N:0:CATTTTAT+GGGGGGGG
CCCGTNGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGAAAAA
+**
I want to remove @NB501309:173:HYW77BGX5:1:11101:15947:1058 1:N:0:CATTTTAT+GGGGGGGG and @NB501309:173:HYW77BGX5:1:11101:15947:1058 1:N:0:CATTTTAT+GGGGGGGG from the fastq file.
Kindly suggest me how to perform.
Thanks in advance
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Bastien Hervé
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written
by
akbioinfo14 •
•
written
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akbioinfo14 •
2 answers
running ver slow sir
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written
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akbioinfo14 •
record=[]
new_file = open('new_no_qual.fastq', 'a')
with open("no_qual.fastq") as f:
for line in f:
if line.startswith("@"):
if len(record) == 4:
new_file.write('\n'.join(record)+"\n")
record=[]
record.append(line.rstrip())
else:
record.append(line.rstrip())
if len(record) == 4:
new_file.write('\n'.join(record))
new_file.close()
Tell me if it's too slow, I'll think about it
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Bastien Hervé
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thank you, but i want to remove the corresponding read from the fastq file only which is not having quality scores.
What did you do to have fastq file with some reads without quality ?
If your file is not that big you can use Biopython :For each record in recordsIf you have qualityWrite record in new fileWhile pooling, the reads quality has missed out, now i have to remove those reads. Kinldy help
I think that you should retry your pooling. There is no reason you loose reads because your pooling missed. If quality was missing in the raw fastq file, you can try to remove these reads from raw fastq file
I repooled it, again the same problem, i think i have missed in the raw file only, Kindly help me how to remove those reads.
You should try this tool to validate your fastq first. Investigate your fastq raw files is the best way to not loose information.
In any way if you want to remove these reads, my script below should do the trick