paired read assignation

[PavelEG]

Hi everyone,

I realized that after performing trimmomatic, I have reads in my file R1_p (forward paired), that aren't in my R2_p (reverse paired) file. The number of reads in both files is the same, what could be happening?

In this case, the first read is found in R1_p but not in the R2_p file. Then the next ids are the same...

head of R1_p file:
@M03132:284:000000000-KM9YY:1:1101:14323:2916 1:N:0:TCGACTTG+AGCCTTAA
GGTACTGGTTGGACAGTGTATCCTCCTTTATCAGGTATTCAATCACATTCGGGAGGTTCTGTAGATTTAGCTATTTTCAGTTTACATTTAGCAGGAACTTCTTCTTTATTGGGTTCT
ATAAATTTTATTACAACTATTTTTAATATGAGAGTTCCTGGAATGGAAATGCATAAAATACCCTTATTTGTATGAGCGATTTTAATAACTGCGTTTTTATTGTTATTATCACTACCT
GTTTTAGCTG
+
AAABBFFFFFBBGGGGGGDGGGHFHHHHHHHHHHHGGHGHHHHHGHFHHHHHGGGGGHHFGGHHGHHHHGHHHHHHHHHBGFFHHFHHHHHHHHFECGHFHFFHBHHHHHHHEGGHG
HHHHFHHHHHHHHHHHHHHHHHGHHHHHGHHFFHHHHHHHHFGHBG2FGHBDDGGGHHGFHFHHHBHHHBGDHEB>G?CHHGHHEHHHBGFFDGGGGEEHHHHHB0G=GBDDG0CBD
DFGHHB/:C;
@M03132:284:000000000-KM9YY:1:1101:18065:2943 1:N:0:ACGACTTG+AGCCGTAA
GGTACTAGTTGGACAGTGTATCCCCCTTTATCAGGAAGTTATTCTCATTCGGGTCCTGCAGTAGATATTGCTATTTTTTCTTTACATTTAGCTGGTATATCTTCAATAGCTGGAGCA
ATAAATTTTATAGTTACAATATTTAATATGCGTTGTAGAGGTTTATCTTTAGATATACTTCCTTTATTTTGTTGAGCTGTTTTATATACAGCATTTTTATTATTATTATCTTTACCT
GTTTTAGCTGGTGCTAT
+
AAAAAFFFFFFFGGGGGGGGGGHHGGGHHHHHHHHHHHHHHHHHHHHHHHHHGHGHHIHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHGHHHHHGHHHHHHHHHHHHHHH
HHHHHHHHHHHHHHHGHHGHHHHHHHHHHHHGEEEFEHHHHBGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHGHHHFFHH
HHHHHHBFHFFGBGHFH

and R2_p:

@M03132:284:000000000-KM9YY:1:1101:18065:2943 2:N:0:ACGACTTG+AGCCGTAA
TAGACTTCGGGATGGCCAAAGAATCAAAATAAATGTTGATACAATATAGGGTCTCCACCACCTTCAGGTTCAAAAAATGTTGTACTAACATTTCTATCAGTTAATAACATAGTAATA
GCACCAGCTAAAAC
+

AAAB5DFBB@DEGCFGGGGCFFGHHGHCFGCFHGGHB5FFGGBGGGBD32FFFGGFCGCCAGFGEFFBFEE5FB1EHBFGBF5DF553@GHHFH4GGB4BBB4FDB@3B33FB4F4
4@4B?10?GB433B
@M03132:284:000000000-KM9YY:1:1101:18951:2977 2:N:0:ACGACTTG+AGCCGTAA
AGACCTCGGGGTGGCCAAAAAATCAGAATAAGTGTTGGTATAATACAGGGTCACCTCCACCTGCTGGGTCAAAG

A>AACFFBBBBGGGFGGGGC22FFH3FBHFBBGFHG22FHFFBHGFD531FFGGEHFGBFCHE1G331FG1355

Many thanks in advance.