Cut the reads.. paired end fastq file

[solaymane]

hello i am new member beginner to the field

[RogerH]

I recently used fastx_trimmer on my data and I can only recommend it.

[dgtnk]

perl is OK
fastx_trimmer provided by FASTX_Toolkit may be faster.

[empyrean]

i use perl.. keep the right end.. and trim the left end.. i already trimmed adapters..

[maubp]

Do you mean keep the left end, or keep the right end?

What is your favourite scripting language (since there are lots of options here, Perl, Python, Ruby, etc)?

[empyrean]

hi.. i have the following 150bp reads.. i would like to cut the bases which are more than 100bp. Also i would like to cut from begining of the read. please let me know any script or program which can do this.

@HWI-DO4456:7:000000000-Z07CL:1:1:15052:1479 1:N:0:GGCTAC
TCCTCAGATTTTTTAGAAAGAGGAGTCTGCTTATAAGATAATGGCATCATTTTGATAGAATCTCCTCGCATTGTTGTAAAACTAATAACAAAGAAGGTTGGTTTTTGTGGTTTTGGTCTCCCGGCCTGAATCCAAGCTTGATGAATACGAA
+
@CCFFFFFHHHHHJJIJJJJJJIJJJJJJJJJIJJJIJJJIJJJJJJJJJJJJIJJJJJJIJGJJJJJJFHHFFFFFEEEEDEDDDDDDDCDDCBDD>@CB?BDDDDDDDCBDDDBBCDDDDDDDBDDDDDDDDDCBCDCBCDDDDEDDDD
@HWI-D04456:7:000000000-Z07CL:1:1:17590:1511 1:N:0:GGCTAC
TTAATTATACTTGTTGGTTTTGGTGGCGGATTAACATGGGGAGCAGTCGCTCTTCGTTGGGGTAAATAAGGACTGAGAGAAAAAAAGGAGTGTATTTTGTGAAGGTAGGGGCACAGTACCGTTGAAGCGTCTAATGAACGTGGAGGGATGG
+