User: Mitra

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Mitra0
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Posts by Mitra

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Comment: C: Converting a bunch or SRA files using fastq-dump split-files
... Great ..that is really helpful. I understand now thats the reason with -l I was getting result but also additional error msg as probably fastq-dump was not dealing well with all that extra information. Thank you very much, S :) ...
written 25 days ago by Mitra0
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Comment: C: Converting a bunch or SRA files using fastq-dump split-files
... Thank you Genomax. Sorry I couldn't reply you yesterday as Biostars restricted my daily comments limit. This time with your suggestion it works :) can you please tell me what is the exact difference in l and 1. I can see from man page -l use a long listing format and -1 list one file per lin ...
written 25 days ago by Mitra0
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Comment: C: Converting a bunch or SRA files using fastq-dump split-files
... yes I am using `for f in `ls -l /Users/medsmit/ncbi/public/sra/*.sra` ; do ./fastq-dump --split-files $f; done` as my command now. ...
written 26 days ago by Mitra0
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Comment: C: Converting a bunch or SRA files using fastq-dump split-files
... Yes the spots looks correct. So I get the fastq results. But I am not sure what are all these messages though ! ...
written 26 days ago by Mitra0
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Comment: C: Converting a bunch or SRA files using fastq-dump split-files
... jean.elbers Thanks for pointing these errors to me.. part of which just got introduced when I wrote this post. Now it seems like its creating fastq files, but unfortunately also creating some strange error: ./fastq-dump : 2.9.0 2018-05-24T12:10:07 fastq-dump.2.9.0 err: item not foun ...
written 26 days ago by Mitra0
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Comment: C: Converting a bunch or SRA files using fastq-dump split-files
... Thanks Genomax. Yes I do have space between -- and split-files in the loop. Also I tried with ls -l After I pass this code bellow: medsmit$ for i in `ls -l /Users/medsmit/ncbi/public/sra/*.sra' ; do ./fastq-dump -- split-files $f; done I only see > As if it entered in any interface ...
written 26 days ago by Mitra0
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Converting a bunch or SRA files using fastq-dump split-files
... I have recently downloaded a bunch of sra files. and i like to convert them to fastq paired reads. It works by doing this : ./fastq-dump --split-files /Users/medsmit/ncbi/public/sra/SRR3501908.sra But I need a way to convert them all together. I was trying this for i in `ls /Users/medsm ...
ncbi sra split-files fastq-dump written 26 days ago by Mitra0 • updated 26 days ago by ATpoint4.4k
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Comment: C: How to match and merge two tables in a effective way where sample names are same
... Thats perfectly what I need. THank you very much cpad0112. Many thanks. Mitra. ...
written 8 months ago by Mitra0
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Comment: C: How to match and merge two tables in a effective way where sample names are same
... No this one only duplicate columns of all datasets by adding.x and .y > dim(A) [1] 6 32 > dim(B) [1] 6 32 > dim(MerAB) [1] 7 63 So not the intended result at all. Thanks anyway. M ...
written 8 months ago by Mitra0
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Answer: A: How to match and merge two tables in a effective way where sample names are same
... My original two datasets dimensiona are 256 by 32 and 270 by 32. All the top data name (32) are same for both. Only the rows are different. I wasnt these teow data combined (added in case of same rows.) Thanks. M ...
written 8 months ago by Mitra0

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