User: ramonaramonawan

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Posts by ramonaramonawan

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(Closed) PCR with 2 cycles gave no products
... Hi guys, As I am going to do the Miseq sequencing. I wanted to run the 1st PCR with 2 cycles, and input the 1st PCR product to the 2nd PCR, which I can run over 20 cycles (I need to test the minimum cycle number of course). To confirm this strategy works, I used 50ng genomic DNA, run the PCR with ...
pcr written 2.8 years ago by ramonaramonawan10
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Comment: C: cutadapt software command to trim the primer sequences
... Thanks a lot, Rohit. I am running another round of sequencing now, and I will try this. See if it works. ...
written 2.8 years ago by ramonaramonawan10
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Comment: C: cutadapt software command to trim the primer sequences
... Hi Rohit, I used the version of cutadapt==1.9.1 I think as i installed from this website : http://cutadapt.readthedocs.io/en/stable/installation.html. I used pair-end data, and the primer sequence is 20bp nucleotides used to amplify the target gene. I did follow the rules of the manual as I unders ...
written 3.1 years ago by ramonaramonawan10
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Comment: C: cutadapt software command to trim the primer sequences
... oh, sorry. It is actually like this: cutadapt -g -o cutadapt -a -o (this is for the reverse primer cutting, but I tried both reverse complementary sequence of the 3´sequence and the 3´sequence without making the reverse complementary, both did not work) As for ...
written 3.1 years ago by ramonaramonawan10
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Comment: C: CRISPResso analysis software
... no, actually the padded sequences are not of fixed length, they range from 0 to 9 nucleotides, it is just for the sequencing sake. ...
written 3.1 years ago by ramonaramonawan10
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Comment: C: How to remove illumina PCR primer 2.01 from RNA-seq samples
... To Juke-34. I have tried, but seems I could get the 3´primers cut off, I use the command cutadapt -a o directory/input file for the reverse primer sequence I hoped to cut, I tried the either the exact sequence of from 5´to 3´, or the reverse complementary one (the same as reverse primer as we or ...
written 3.1 years ago by ramonaramonawan10
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cutadapt software command to trim the primer sequences
... Hi guys, I am trying to trim my primer sequences off my sequence data. I wrote the command with cutadapt. cutadapt -g F-primer sequence -o output file name directory of input file/input file name it could cut the forward primer off. but if I use the same command for reverse primers cut ...
sequencing written 3.1 years ago by ramonaramonawan10 • updated 2.4 years ago by a.a.kechin20
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CRISPResso analysis software
... Hi, I got the sequencing data of Miseq, and tried to use CRISPResso to do the analysis since I am using CRISPR to cut the target gene. However, my sequencing molecules do not start with the same nucleotide since I also add some barcodes beyond my PCR primers with different length. I tried to trim th ...
sequencing written 3.1 years ago by ramonaramonawan10

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