User: bharath.mh24

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Posts by bharath.mh24

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Comment: C: Many to Many alignment of Large number of sequences
... I tried BOWTIE 2. My reads are all 80bp long. Any suggestions?? ...
written 18 months ago by bharath.mh240
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Comment: C: Many to Many alignment of Large number of sequences
... I did try working on debugging that for a while. But I couldn't quite figure anything out! Could not think of anything! Thank You ...
written 19 months ago by bharath.mh240
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Comment: C: Many to Many alignment of Large number of sequences
... Server offering computing cluster with processor Intel Xeon E5-2698v3 16C/32T 2.30 Ghz, 63 nodes and 32 cores. Computing resources dont seem to be the problem. I would think I need to change the command a bit from just blastn. Thank You Very Much ...
written 19 months ago by bharath.mh240
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Comment: C: Many to Many alignment of Large number of sequences
... Will I be able to blast so many sequences at once? Is there some way I could make use of multiple cores or speeden it up? Because I tried this and it is always stuck. Thank You ...
written 19 months ago by bharath.mh240
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Comment: C: Many to Many alignment of Large number of sequences
... I did try that! But I kept getting * in my SAM output! Is there any other way this could be done? I have been struggling with this for a while now. Thank You ...
written 19 months ago by bharath.mh240
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Comment: C: Many to Many alignment of Large number of sequences
... The dataset I have is actually single end 5C reads! There are effectively not many tools to use for single end 5C data! So BLAST seems like the most viable option! Thank You ...
written 19 months ago by bharath.mh240
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Comment: C: Many to Many alignment of Large number of sequences
... Yes, it is! 5C but I have been recommended to align the reads!! Thank You ...
written 19 months ago by bharath.mh240
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Comment: C: Many to Many alignment of Large number of sequences
... But how do you blast one set of sequences with another set? Basically, a many to many blast. ...
written 19 months ago by bharath.mh240
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Comment: C: Many to Many alignment of Large number of sequences
... Oh, Okay. I shall try it! Thank You very much!! ...
written 19 months ago by bharath.mh240
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Comment: C: Many to Many alignment of Large number of sequences
... Yes, but then the output format would be too large to access. I am not very skilled in programming, so any suggestions would be helpful!! ...
written 19 months ago by bharath.mh240

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