@SRR3117565.1.1 1 length=100
NCAAAACAGCTCTCCCTCCTTTGATCTGATGGTCTGCAGAGGTCCTCAAATCCACACACTGCCACTCTTCAAGACCAACCACTGGGCCTTCTTAATCTCA
+SRR3117565.1.1 1 length=100
#1=BDDDDHFHHAHDE?GFEEDHG@HFHEECDCGHE:FDFHD*?DHFD<GEDEGIIIIIA=AFFGACHDH>EHHF>;;B<;A;>=A=??@CCCC>5>>AC
@SRR3117565.2.1 2 length=100
NTCCTGACTCACACGCCACAACCATGACTGGCTCAGCTCCCTTAATTCCAGCTTCCCTTACATGACGCAATTCCTTCTCAGATTCGGGTTTTCAGCTGAG
+SRR3117565.2.1 2 length=100
#4BDFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHHFEFEEEEEEDDEDDDDDDDDBDDDDDDDDDDD
Example of a fastq file in read 2 is as follows:
@SRR3117565.1.2 1 length=100Following script fix it such that both fastq files (corresponding to the paired sequencing reads) of sample SRR3117565 have similar read names.
TGGTTTTTTTTTTTGTCCCTCAAATTTTTGGACTCCGTAACATCAACCAGTTTGGAGTGGGATGACAGAGAGAATGCCCAATTTTGTGAGGCCCATGATT
+SRR3117565.1.2 1 length=100
59(2(3(2=9/>;?/=)))))().8<8))'-).6..8:(',)..)(((((-(53/(,,(((((,(((+(+(+2((((+((+((+23++(+2+++2++(((
@SRR3117565.2.2 2 length=100
CTGGCTTGTTATAACGCAAAGCTTGGTTGTTTATGCAACTCTATCTTAAGAACTGCCCAGCCTCAGCTGAAAACCCGAATCTGAGAAGGAATTGCGTCAT
+SRR3117565.2.2 2 length=100
CCCFFFFFHHHHHJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJJJJJJJJJJJIJJJJHIJJJHHHHHFFFFFDDDDDDDDEDDDDDDDDDDDDDDDDB
nohup sed 's/\([@|\+]SRR.*\)\.1.*/\1/' ./SRR3117565_1.fastq > ./SRR3117565_1.correctId.fastq &
nohup sed 's/\([@|\+]SRR.*\)\.2.*/\1/'./SRR3117565_2.fastq > ./SRR3117565_2.correctId.fastq &
nohup sed 's/\([@|\+]SRR.*\)\.2.*/\1/'./SRR3117565_2.fastq > ./SRR3117565_2.correctId.fastq &
Modify read names in bam files in Linux
In this example I would show how to remove ":1" and ":2" at the end of the query/read-names that show the first and the second paired read. If the reads/query names start with "SRR" the following scripts can be used:
samtools view ./file.bam | perl -pe 's/(^SRR.*?):[1-2]\t/\1\t/g' > ./file.sam
cat ./file.sam | samtools view -bS - > ./file_modified.bam
cat ./file.sam | samtools view -bS - > ./file_modified.bam
or all together the following script can be run:
samtools view ./file.bam | perl -pe 's/(^SRR.*?):[1-2]\t/\1\t/g' | samtools view -bS - > ./file_modified.bam
In the end the string modification may mix up the header of the bam files, as a solution to the problem the header could be seprataed the then reattached as following:
samtools view -H /netapp/seqRawData/eugeneMouse/DIV0.bam > /netapp/seqRawData/eugeneMouse/DIV0_head.sam &
samtools view /netapp/seqRawData/eugeneMouse/DIV0.bam | perl -pe 's/(^.*?):[1-2]\t/\1\t/g' > /netapp/seqRawData/eugeneMouse/DIV0M.sam &
cat /netapp/seqRawData/eugeneMouse/DIV0_head.sam /netapp/seqRawData/eugeneMouse/DIV0M.sam |samtools view -bS - > /netapp/seqRawData/eugeneMouse/DIV0M.bam
samtools view /netapp/seqRawData/eugeneMouse/DIV0.bam | perl -pe 's/(^.*?):[1-2]\t/\1\t/g' > /netapp/seqRawData/eugeneMouse/DIV0M.sam &
cat /netapp/seqRawData/eugeneMouse/DIV0_head.sam /netapp/seqRawData/eugeneMouse/DIV0M.sam |samtools view -bS - > /netapp/seqRawData/eugeneMouse/DIV0M.bam
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