User: Moneeb Bajwa

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Posts by Moneeb Bajwa

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Finding orientation of single-ended reads (R or F)
... So would I put F (forward) for when Trinity asks for Ss_lib_type when I am aligning? ...
written 1 hour ago by Moneeb Bajwa0
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Comment: C: Finding orientation of single-ended reads (R or F)
... But I can't find the manual for that; the only one I can find is for paired-end reads ...
written 2 hours ago by Moneeb Bajwa0
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Comment: C: Finding orientation of single-ended reads (R or F)
... I am trying to do a de-novo assembly with Trinity ...
written 2 hours ago by Moneeb Bajwa0
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Finding orientation of single-ended reads (R or F)
... Hello, How would I find out whether my single-ended reads are forward or reverse? Here are the SRA reads I used: https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=434667. Thank you! ...
sequence assembly next-gen rna-seq written 2 hours ago by Moneeb Bajwa0 • updated 2 hours ago by h.mon16k
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Comment: C: Trimmomatic SureSelect protocol
... In the manual you gave, I see it is for SureSelect QXT: https://www.agilent.com/cs/library/usermanuals/public/G9682-90000.pdf; but mine are SureSelect Strand Specific. Does that matter? Mine are also single-ended reads. ...
written 5 days ago by Moneeb Bajwa0
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Comment: C: Trimmomatic SureSelect protocol
... Is this something that is usually done? Is it possible it is a different adapter? ...
written 8 days ago by Moneeb Bajwa0
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Comment: C: Trimmomatic SureSelect protocol
... Yes i just fixed my last comment; you can see it now ...
written 9 days ago by Moneeb Bajwa0
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Comment: C: Trimmomatic SureSelect protocol
... @DRR089573.1 J00158:10:H7CTLBBXX:1:1101:30594:1226 length=36 NTTGGGGGGAAGGTCTGGATCCAAGATGGTGATGAT +DRR089573.1 J00158:10:H7CTLBBXX:1:1101:30594:1226 length=36 # ...
written 9 days ago by Moneeb Bajwa0
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Comment: C: Trimmomatic SureSelect protocol
... No I did fastq-dump ...
written 10 days ago by Moneeb Bajwa0
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Comment: C: Trimmomatic SureSelect protocol
... I am not really understanding...when I use that grep command on one of the files I get 0 occurrences. These are the SRA sequences: https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=434667. I do get 34 occurrences in one of the files if I use just CTGTCTCTTGATC. Not sure how ...
written 14 days ago by Moneeb Bajwa0

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