User: Himanshu Bhusan Samal

Reputation:
20
Status:
New User
Location:
Germany/Berlin/Max Delbruck Center for Molecular Medicine
Twitter:
samalbioinfo
Last seen:
7 months ago
Joined:
2 years, 10 months ago
Email:
h***************@gmail.com

Posts by Himanshu Bhusan Samal

<prev • 15 results • page 1 of 2 • next >
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Comment: C: bash command for trimming and filtering .fastq files
... Thank you so very much Sterck! I was trying that only. It's working the way you suggested (with -O 2 parameter). Couldn't post my message because I have limitation of sending 5 message per 6 hours, so reached the limitation. Sorry for the delay. I am really thankful for both of your effort, thank yo ...
written 7 months ago by Himanshu Bhusan Samal20
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Comment: C: bash command for trimming and filtering .fastq files
... Thank you so very much Sterck! I was trying that only. It's working the way you suggested (with -O 2 parameter). Couldn't post my message because I have limitation of sending 5 message per 6 hours, so reached the limitation. Sorry for the delay. I am really thankful for both of your effort, thank yo ...
written 7 months ago by Himanshu Bhusan Samal20
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Comment: A: bash command for trimming and filtering .fastq files
... Yes, I was trying to bold the rest sequence after TA, (sequence which I want to keep after trimming, just to visualize for you) that's why '**'. And, randomly I have copied pasted the .fastq sequences (from a huge .fastq file), that's why the length is not matching to the quality of sequence. In the ...
written 7 months ago by Himanshu Bhusan Samal20
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Comment: C: bash command for trimming and filtering .fastq files
... I am not getting this error when I am trying with any different/long adapter. Code is same only. I have used cutadapt for adapter trimming several times, but this error is for the first time when I am trying to trim only two base, TA. Thats why I thought here maybe it's not possible with cutadapt, t ...
written 7 months ago by Himanshu Bhusan Samal20
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Comment: C: bash command for trimming and filtering .fastq files
... Thanks for your reply. Of course, I read the manual and had tried the same that you mentioned. Since I was getting error, thought of trying in different way, if it is possible. Since it's working for you, maybe some problem from my side. I am trying to sort that, thanks! Trimming 1 adapter(s) ...
written 7 months ago by Himanshu Bhusan Samal20
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Comment: C: bash command for trimming and filtering .fastq files
... Hello, thanks very much for both of your response. Yes, I would like to trim from 5' end (from left side up-to/including TA). Ex- 'GGCGATGCGGCGGCGTTA' from the first read. Then want to remove if any reads having length <40. Previously I have tried cutadapt, but it's not filling the purpose as t ...
written 7 months ago by Himanshu Bhusan Samal20
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Comment: C: bash command for trimming and filtering .fastq files
... Hello, thanks very much for both of your response. Yes, I would like to trim from 5' end (from left side up-to/including TA). Ex- 'GGCGATGCGGCGGCGTTA' from the first read. Then want to remove if any reads having length <40. Previously I have tried cutadapt, but it's not filling the purpose as t ...
written 7 months ago by Himanshu Bhusan Samal20
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Comment: C: bash command for trimming and filtering .fastq files
... Thanks for your suggestions. ...
written 7 months ago by Himanshu Bhusan Samal20
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bash command for trimming and filtering .fastq files
... Hello everyone, I need little help to work with the genomic DNA seq. I would like to trim the reads (.fastq files) until first 'TA' position. And then, want to remove all the reads having length <40bp. It would be helpful if someone could share some useful commands to do the same. Thanks very mu ...
filtering fastq files written 7 months ago by Himanshu Bhusan Samal20 • updated 7 months ago by RamRS21k
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Comment: C: mass-spec data analysis pipeline
... Thanks for the info. Yes, it's a predicted protein. I would try to do the same as you mentioned. Thank you! ...
written 7 months ago by Himanshu Bhusan Samal20

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