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How to trim polyT from the front #597

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ayash338 opened this issue Feb 20, 2025 · 2 comments
Open

How to trim polyT from the front #597

ayash338 opened this issue Feb 20, 2025 · 2 comments

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@ayash338
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In RNA-seq data, some reads have poly A at the end, some reads have poly T at the front.
How can I remove the polyT from the front of reads?

@sfchen
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sfchen commented Feb 20, 2025

Can you show me some reads here?

@ayash338
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Thank you for your reply.
The following sequences are from my fastq file.
TTTTTTTACCAAGGACAAGAATTACTGGTTCACATAAAACACAAGAGATCTGAAAACACACTTCAGAGGAACATAGCAGGAAAATCCTTTTTAGCGACTACAGCTAGTAGGATGCTTCACTGGAAATTGATAAAACAAGTGTTGCATCTTA
TTTTTTTCAGTGTCTTGTAGCATGTCTTCTTCAGATAATCTGAAAATTGTGACAGGGCTACCCAAATTGATGTTATGATGATTGTCTTCAGAGATATCTCTATTTTGACCTTCCGAATCTTCTTCTGAAAGCTCTAGGTTTCTTTCAAAAG
TTTTTTTGTGTATATAGACTTGCAGTTGCAAACCGAATTACATGCGTGGTGTCTCATAGACGTACAAATTCCACAGGCTGAGGCTTTCCTTTCTGCATCCAACCAAGCCCTGCGGTAATACATCTGGTCGACACGACAAAACCATGTTCAA
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATATATATCTTATATACTTTTTTAAAATTAAAAAAAAAAC
TTTTTTTTTTTTTTTTTTTTTTGGTGCAATGTTGGTTCTCTTTCTTTTAATTTTTACAAAGCTGGCAGCAGCATTCTTTAGCTATATACTTCTGTATGTAAAGTTGTAAAAAGTTTGGAGAAAAAAACTAGCATTGGTGACACAAAACTAT
TTTTTTTCCAGTCCAAAAAAAAAAATCCCATCACTCTTTCAATCGGAGTTGCAATGGTTCGCTCAGCACAGTAACTTGTAAGCAAGCAAACAGAACATCAATAGCCAAGACTTTAGCATACGGAACCAGTACGCACTCCTGATACACGCGA
TTTTTTTTTTTTTTTAGCAAGAATCAGACTTTAATGCATGACAGAATCAGATCTCCAATAAATAACACACCGCAGCATTTTACGTCTACATGCACAAAGGCAAAACACAAGAGAACGGCTTAACATCAGATGTCAAATGTTTTCCTACTCC
TTTTTTTTTTTTTTCATAAAATCTCTGTAGATCGATAATGCAAAGAAACTTCTTACCAAAAAAAATACTATTAGCTTATATTGTTCCAAAAATAACCTAAAGCCCTAGCTAGAGTCTAAAGTAACTCGATGCCTCCATCTACTAGTTGGAG

I don't know much about RAN-seq, but when the cDNA fragment contains poly A and the 1st cDNA is sequenced, the poly T is read at the head, right?
So I wish there is a command option which trim the polyT or polyX at the head.
Thanks in advance.

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