User: tcf.hcdg

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tcf.hcdg60
Reputation:
60
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Location:
European Union
Last seen:
2 weeks, 2 days ago
Joined:
2 years, 11 months ago
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Posts by tcf.hcdg

<prev • 88 results • page 1 of 9 • next >
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Comment: C: Merging two fastq.gz files
... I used the following and it worked: R1 for ((num=71; num<=94; num++)); { cat 22"$num"*{L001,L002}_R1_001.fastq.gz > "22${num}_merged_R1_001.fastq.gz" ;} R2 for ((num=71; num<=94; num++)); { cat 22"$num"*{L001,L002}_R1_001.fastq.gz > "22${num}_merged_R1_001.fastq.gz" ;} ...
written 21 days ago by tcf.hcdg60
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Comment: C: Merging two fastq.gz files
... And What about " 1. Why only two output files are generated? " ...
written 27 days ago by tcf.hcdg60
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Merging two fastq.gz files
... Hello, I have 96 *fastqc.gz raw read files from 24 samples. Each sample was sequenced on two lanees for each pair. I would like to merge reads for each pair from both lanes into one output file with same name identifier from sample file name (2271_merged_R1_001.fastq.gz). File names are in ...
merging fastq written 28 days ago by tcf.hcdg60 • updated 27 days ago by igor6.0k
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Comment: C: How to read a loop over to read a file in a folder for many folders
... Thanks. It worked for dir in /home/tb44227/nobackup/small_RNAseq_260917/support.igatech.it/sequences-export/536-RNA-seq_Disco_TuDO/delivery_25092017/*/ ; do cd "$dir" for file in ./*.fastq.gz ; do java -jar trimmomatic-0.36.jar SE -threads ${PBS_NUM_PPN} -phr ...
written 11 weeks ago by tcf.hcdg60
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Comment: C: How to read a loop over to read a file in a folder for many folders
... It's normal fastq file tb44227@lido-gw02:~/nobackup/small_RNAseq_260917/support.igatech.it/sequences-export/536-RNA-seq_Disco_TuDO/delivery_25092017/754_1>zcat 754_1_ATCACG_L006_R1_001.fastq.gz | head @SEQILMN03:400:CBEFMANXX:6:1101:1200:1889 1:N:0:NTCACG NACTCGGATAACCGTAGTAATTCTAGAGCTA ...
written 11 weeks ago by tcf.hcdg60
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How to read a loop over to read a file in a folder for many folders
... I have 15 folders and each folder contained a *.gz file. I would like to use trimmomatics for filtering all the files. For this I would like to write something that can open that folder and read the that specific file and then do the filtering as specified in the code and finally save the results w ...
trimmomatic filtering multiple files written 11 weeks ago by tcf.hcdg60 • updated 11 weeks ago by shenwei3563.6k
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Comment: C: How to merge BLAST XML output from different database?
... As I mentioned in the previous comment, because fo the GNU parallel each file has multiple blast xml header and footer. I remove the repeated header and footer from the file and then tried your script, it worked and merged two files. But the resultant file in in one line blastx ...
written 13 months ago by tcf.hcdg60
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Comment: C: How to merge BLAST XML output from different database?
... I think the script should be like: First it should merge all the resulted xml files that was generated for one database 1 let's say in this case merge all 31 files of database1 Then it should some how sort the xml files. The reason to sort is queries are not insorted format,because I used GNU pa ...
written 13 months ago by tcf.hcdg60
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Comment: C: How to merge BLAST XML output from different database?
... I am sorry I couldn't respond earlier because of my limited posting option. Well, Itried and the output is like that: tb44227@lido-gw02:~/nobackup/jvarkit>xmllint ~/nobackup/Radula/Trinity_1500k_Radula_lnr_hededt_split/merging_xml_db1_db2/03_Rma_trn1500k_nrbx5_hsp20_e3_dbp1 > /dev ...
written 13 months ago by tcf.hcdg60
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Comment: C: How to merge BLAST XML output from different database?
... java -jar dist/mergeblastxml.jar ~/nobackup/Radula/Trinity_1500k_Radula_lnr_hededt_split/merging_xml_db1_db2/03_Rma_trn1500k_nrbx5_hsp20_e3_dbp1 ~/nobackup/Radula/Trinity_1500k_Radula_lnr_hededt_split/merging_xml_db1_db2/03_Rma_trn1500k_nrbx5_hsp20_e3_dbp2 > output.xml [INFO][MergeBlastX ...
written 13 months ago by tcf.hcdg60

Latest awards to tcf.hcdg

Popular Question 19 days ago, created a question with more than 1,000 views. For How to do multiple blast for multifasta file/s with command line blast
Popular Question 21 days ago, created a question with more than 1,000 views. For How to do multiple blast for multifasta file/s with command line blast
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Popular Question 9 months ago, created a question with more than 1,000 views. For How to do multiple blast for multifasta file/s with command line blast
Popular Question 9 months ago, created a question with more than 1,000 views. For sequence extraction from multifast file using IDs in another text file
Popular Question 11 months ago, created a question with more than 1,000 views. For standalone blast , database error
Popular Question 12 months ago, created a question with more than 1,000 views. For standalone blast , database error
Popular Question 16 months ago, created a question with more than 1,000 views. For standalone blast , database error
Popular Question 19 months ago, created a question with more than 1,000 views. For unique sequence IDs from fasta file

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