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Old 12-18-2011, 03:36 AM   #1
empyrean
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Default Cut the reads.. paired end fastq file

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.

Code:
@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
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Old 12-18-2011, 01:02 PM   #2
maubp
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Default

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)?
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Old 12-18-2011, 01:42 PM   #3
empyrean
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i use perl.. keep the right end.. and trim the left end.. i already trimmed adapters..
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Old 12-18-2011, 05:57 PM   #4
dgtnk
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perl is OK
fastx_trimmer provided by FASTX_Toolkit may be faster.
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Old 12-18-2011, 09:35 PM   #5
RogerH
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I recently used fastx_trimmer on my data and I can only recommend it.
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Old 06-05-2012, 08:52 AM   #6
solaymane
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hello i am new member beginner to the field
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