User: hasche89

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hasche890
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Posts by hasche89

<prev • 6 results • page 1 of 1 • next >
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How to carry out quality control using Trimmomatic on SRA reads of SAGE-RNASeq?
... I have carried out a FASTQC analysis on raw reads of SAGE-RNASeq experiment from SRA database. Numerous over-represented sequences have turned up pertaining to Illumina single end adapters and primers; paired end pcr primers, indexes etc (See black quotes). Currently, I am confused about how to car ...
trimmomatic sage qc rna-seq fastqc written 6 months ago by hasche890
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(Closed) I have a fasta file with 2000 sequences (big.fasta) and a text file with 70 sequence ids (ids.txt). How can I remove (or cut and paste) the sequences in ids.txt from the big.fasta file?
... I have a fasta file with 2000 sequences (big.fasta) with transcripts. I also have a text file with 70 sequence ids (ids.txt) present between those 2000 sequences. I want to remove the sequences in ids.txt from the big.fasta file; thus creating a fasta file with 1930 sequences free of the ids from ...
perl bioperl samtools rna-seq bash written 21 months ago by hasche890 • updated 21 months ago by thackl2.3k
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Comment: C: Extracting specific sequences from a big fasta file using ids of the sequences t
... Thanks for the commands. I am a beginner in this field. Can you please tell me what does each component of your command does? Thanks.   ...
written 21 months ago by hasche890
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Comment: C: Extracting specific sequences from a big fasta file using ids of the sequences t
... Hi, thanks for the reply. I have a text file with the ids I want to exclude from the bigger file. How can I provide the txt file as an input to the awk command provided above?   ...
written 21 months ago by hasche890
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(Closed) How to create the environment variables for BioPerl? How to override them in Ubuntu 12?
... How to create environment variables BIOPERL_INDEX and BIOPERL_INDEX_TYPE in Ubuntu 12?   Also, can someone provide me the command line for how to override both of these environment variables? Thanks. ...
perl ubuntu bioperl written 21 months ago by hasche890
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Extracting specific sequences from a big fasta file using ids of the sequences to be excluded
... I have a huge fasta file of around 20 GB size. I also have some sequence IDS from the same fasta file in text format. Now, I want to retrieve those sequences which don't have those particular ids in the text file. How shall I proceed? I use Ubuntu 12. I am a novice and have very little knowledge of ...
perl faidx samtools bioperl rna-seq written 21 months ago by hasche890 • updated 21 months ago by Brian Bushnell12k

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