1. UNIX for Dummies Questions & Answers

Hi Everyone, I am new in the world of UNIX and Shell scripting. I am working with a sequence file that looks like this: >contig00001 length=128 numreads=2 aTGTGCTGGgTGGGTGCCTGTTgCCccATGCTCCAGTtCAGGATTtCAGGCAttCTCATG TCCAGCATTTCTATTTAATCCTGCTGCTGGACTTGGGTGGtCTCAGTCtGGGAAGTGAGC tGTCTGTG... (8 Replies)

2. UNIX for Dummies Questions & Answers

Hi I have an alignment file (.fasta) with ~80 sequences. They look like this- >JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0 GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)

3. Shell Programming and Scripting

Hi, I am trying to remove lines once a string is found till another string is found including the start string and end string. I want to basically grab all the lines starting with color (closing bracket). PS: The line after the closing bracket for color could be anything (currently 'more').... (1 Reply)

4. UNIX for Dummies Questions & Answers

I have fasta files with multiple sequences in each. I need to change the sequence name headers from: >accD:_59176-60699 ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA >atpA_(reverse_strand):_showing_revcomp_of_10525-12048 ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)

5. Shell Programming and Scripting

Hi, I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help . input > fefrwefrwef X900 AGAGGGAATTGG AGGGGCCTGGAG GGTTCTCTTC > fefrwefrwef X932 AGAGGGAATTGG AGGAGGTGGAG GGTTCTCTTC > fefrwefrwef X937... (2 Replies)

6. Shell Programming and Scripting

Hello, I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)

7. Shell Programming and Scripting

HI, I have a Complete genome fasta file and I have list of sub sequence regions in the format as : 4353..5633 6795..9354 1034..14456 I want a script which can mask these region in a single complete genome fasta file with the alphabet N kindly help (2 Replies)

8. Shell Programming and Scripting

I would like to take a fasta file formated like >0001 agttcgaggtcagaatt >0002 agttcgag >0003 ggtaacctga and use command line perl to move the all sample gt 8 in length to a new file. the result would be >0001 agttcgaggtcagaatt >0003 ggtaacctga cat ${sample}.fasta | perl -lane... (2 Replies)

9. UNIX for Beginners Questions & Answers

I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position, AAGCZ-N16-AAGCZ Z represents A, C or G (Except T) N16 represents any of the four... (3 Replies)

10. UNIX for Beginners Questions & Answers

Below are my custom period start and end dates based on a calender, these dates are placed in a file, for each period i need to split into three weeks for each period row, example is given below. Could you please help out to achieve solution through shell script.. File content: ... (2 Replies)