User: simplyphage

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Posts by simplyphage

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Comment: A: Removing UMI with UMI tools?
... Thank you @genomax and @i.sudbery for your inputs. ...
written 5 weeks ago by simplyphage0
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Comment: C: Removing UMI with UMI tools?
... Final Command that worked for us: umi_tools extract --stdin=BU243_S1_L001_R1_001.fastq.gz --log=withonesubs2.log --stdout=processed_reads_3.fa.gz --extract-method=regex --bc-pattern='.+(?PAACTGTAGGCACCATCAAT){s<=2}(?P.{12})(?P.+)' ...
written 5 weeks ago by simplyphage0 • updated 5 weeks ago by genomax62k
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Comment: C: Removing UMI with UMI tools?
... I gave it a try, but the no. of regex matches i got is incredibly low ! 2019-01-15 18:59:01,497 INFO Input Reads: 5442010 2019-01-15 18:59:01,497 INFO regex does not match read1: 5438362 2019-01-15 18:59:01,497 INFO regex matches read1: 3648 2019-01-15 18:59:01,497 INFO Reads output: 364 ...
written 5 weeks ago by simplyphage0
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Comment: C: Removing UMI with UMI tools?
... Yup, The first one. Everything before 3' adaptor is miRNA Seq. ...
written 5 weeks ago by simplyphage0
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Comment: C: Removing UMI with UMI tools?
... Yeah, we will discard those. Going through the data 96% of the seq. contain RT primer, which is workable for us. Thanks again ...
written 5 weeks ago by simplyphage0
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Comment: C: Removing UMI with UMI tools?
... Yeah, that seems to be the only viable option. ...
written 5 weeks ago by simplyphage0
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Comment: C: Removing UMI with UMI tools?
... No, No. 2 is supposed to be the 3 primer Adapter. and No. 4 is supposed to be the RT primer RT Primer is followed by the Universal adapter, which varies in length. If I remove 2 and 4 and extract UMI, I am still left with the Universal adapter, which varies in length. ...
written 5 weeks ago by simplyphage0
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Comment: C: Removing UMI with UMI tools?
... Coudn't get access to the cluster..but i tried the same thing with Cutadapt and Trim_trim galore. But there's a problem now...I noticed that some of the sequences (Example:The second sequence) don't have the RT primer attached. How should i proceed with these type of sequences? SN526:340:HTLWL ...
written 5 weeks ago by simplyphage0 • updated 5 weeks ago by genomax62k
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Comment: C: Removing UMI with UMI tools?
... Sorry, i did try to run it on my laptop but it turned off..due to lack of memory or something i believe. I will get back to you once i get access to the cluster. ...
written 5 weeks ago by simplyphage0
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Comment: C: Removing UMI with UMI tools?
... Yeah, that seems rational. I am relatively new to the sequencing world. So, Thank you so much. I will give it a try. Just a quick question. Can i also do the same thing with trim galore as well? ...
written 5 weeks ago by simplyphage0

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