on what basis the tool trimmomatic works? .... on what basis we need to trim the FastQc Data?
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Scan sequence data/match adapter sequences to sequence data/trim adapter sequences as needed.
If FastQC reports presence of Illumina adapters in your sequence (which can happen if you have adapter dimers or inserts smaller than sequence length which leads to read-through into adapters) then you should trim your sequences. Trimming based on quality should not be needed unless you have really bad quality (Q10 or less) data.
Take a look at bbduk.sh from BBMap suite instead of/in addition to Trimmomatic for scanning/trimming sequence data. -
TRimmomatic
I am from computer science department...this is the sequence we need to trim.
GGTGATACGGTTANATTAATGTACAAAGGTCAACC
AB@B?AAB?B@B<!8@CA@@<BA>=:<17+6=<9<
CAAATTATAAAGCNCATTTAAGTCATCGACAAAAG
B>:8ABCBBAB3?!>ABBA;71?@AB?)=?;68-4
TATAATGCATCGTNATGGAATCCTTGTTCTACATA
BCCA=B?CBBC@,!8CB???A?BB<<A@BBA:7?A
TCAACAATTGGTTNTTTACCTTTTAAAAATAAATT
BB@=AABBB@><;!?BBAAABBB?:96><<@>>>@
AGAAGTTTGCAAANTTTTCAACAAATGATGCAGTA
B@=;ABBB<BA>6!?CCCCBB@@;AB?@A;@?5?@
please explain us what is all we need to remove from this sequences.........we need to develop a tool like trimmomatic.......Comment
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Do not post multiple times posing as different people again, or you will be banned. Consider this your only warning.Comment
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no i haven't posted multiple times...please provide solution for above questionComment
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First of all the sequences posted are not in proper fastq format (if that is what you have been given). Check this Wikipedia entry for description (and proper format) for fastq.Originally posted by VEERESH SHENOY View Post
You would need to keep this format intact after you scan the sequence lines for presence of sequences you want to remove. When trimming you would generally be taking out entire 3'-end (all the way to the right end) of sequence once you locate and identify the sequence you are searching for. You would also need to trim the quality score line (4th line) to match the length of the sequence (2nd line) that will remain after trimming.
Since you know about trimmomatic you can find the manual for the program. Read through it (and the publication) to get additional details.Comment
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Perhaps a classmate had also posted an identical sequence block in this thread. I assume this is a common class assignment?Originally posted by VEERESH SHENOY View PostComment
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