User: anikcropscience

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Posts by anikcropscience

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Comment: C: Trimmomatic output giving error message.
... Thank you very much for helping me out. ...
written 29 days ago by anikcropscience30
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Comment: C: Trimmomatic output giving error message.
... After running your command, I got the following output: -rw-r--r-- 1 adutta staff 421M Jul 12 22:06 SRR4907761_1.fastq.gz -rw-r--r-- 1 adutta staff 987M Jul 12 21:05 SRR4907762_1.fastq.gz -rw-r--r-- 1 adutta staff 697M Jul 12 20:37 SRR4907763_1.fastq.gz -rw-r--r-- 1 adu ...
written 29 days ago by anikcropscience30
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Comment: C: Trimmomatic output giving error message.
... Hi, yes I am copying the script from somewhere. But they do not explain it. So after I run the first step as you showed, I get the following output: Raw_seq adutta$ for infile in *_1.fastq.gz > do > base=$(basename ${infile} _1.fastq.gz) > echo "$infile $base" > ...
written 29 days ago by anikcropscience30
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Comment: C: Trimmomatic output giving error message.
... Hi, so I added that command you suggested, but it still produces the same message. Nothing has changed. Any further suggestions, please? ...
written 29 days ago by anikcropscience30
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Comment: C: Trimmomatic output giving error message.
... So should I write `${base}_1.fastq.gz` before the `${base}_2.fastq.gz`? ...
written 29 days ago by anikcropscience30
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Comment: C: Trimmomatic output giving error message.
... How can I do that? Like just type that command after the "for...." and before "do" command? ...
written 29 days ago by anikcropscience30
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Trimmomatic output giving error message.
... Hello, I am running Trimmomatic for trimming paired-end whole-genome sequence data in a loop. The code is the following: adutta$ cd /Users/adutta/Desktop/Pangenome_kmer_paper/Raw_seq adutta$ for infile in *_1.fastq.gz > do > ...
genome next-gen snp sequencing written 29 days ago by anikcropscience30
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Comment: C: Pipeline for creating a SNP dataset from scratch
... Thank you very much for those two informative links. Yes, I can feel the difficulty level already. ...
written 4 weeks ago by anikcropscience30
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Comment: C: Pipeline for creating a SNP dataset from scratch
... Thanks a lot. I will check those. ...
written 4 weeks ago by anikcropscience30
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Comment: C: Pipeline for creating a SNP dataset from scratch
... Not actually thrown, I will get help later on. But I want to try out myself first. As there are quite a few approaches and tools, I was not sure which one to use. That is why I asked for some tutorials. I do not expect anyone to teach me to step by step procedure. I was trying to get some links for ...
written 4 weeks ago by anikcropscience30

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