<jupyter_start><jupyter_text>Try properly fastq-dumped data<jupyter_code>%%bash
# SRR629563 = U-2 OS cell line
Trinity --seqType fq --max_memory 60G \
    --left /mnt/data/fastq_dump_v2/SRR629563_1.fastq \
    --right /mnt/data/fastq_dump_v2/SRR629563_2.fastq \
    --output /mnt/data/trinity-output/fastq_dump_v2/u2os/trinity-output \
    --CPU 16 --verbose --workdir /mnt/data/trinity-workdir
ls -lha /mnt/data/trinity-output/fastq_dump_v2/u2os/trinity-output
ls -lhStr /mnt/data/trinity-output/fastq_dump_v2/u2os/trinity-output
! head /mnt/data/trinity-output/fastq_dump_v2/u2os/trinity-output/Trinity.fasta
! head /mnt/data/trinity-output/fastq_dump_v2/u2os/trinity-output/Trinity.fasta.gene_trans_map
! cat /mnt/data/trinity-output/fastq_dump_v2/u2os/trinity-output/Trinity.timing
cd /mnt/data/trinity-output/fastq_dump_v2/u2os/trinity-output
ls -lha
cat both.fa.read_count
cat inchworm.kmer_count
! head jellyfish.kmers.fa.histo
! wc -l jellyfish.kmers.fa.histo
! tail jellyfish.kmers.fa.histo
! man grep<jupyter_output>GREP(1)                     General Commands Manual                    GREP(1)

NNAAMMEE
       grep, egrep, fgrep, rgrep - print lines matching a pattern

SSYYNNOOPPSSIISS
       ggrreepp [_O_P_T_I_O_N_S] _P_A_T_T_E_R_N [_F_I_L_E...]
       ggrreepp [_O_P_T_I_O_N_S] [--ee _P_A_T_T_E_R_N]...  [--ff _F_I_L_E]...  [_F_I_L_E...]

DDEESSCCRRIIPPTTIIOONN
       ggrreepp searches the named input _F_I_L_Es for lines containing a match to the
       given _P_A_T_T_E_R_N.  If no files are specified, or if the file “--” is given,
       ggrreepp  searches  standard  input.   By default, ggrreepp prints the matching
       lines.

       In addition, the variant programs eeggrreepp, ffggrreepp and rrggrreepp are  the  same
       as  ggrreepp --EE,  ggrreepp --FF,  and  ggrreepp --rr, respectively.  These variants are
       deprecated, but are provi[...]<jupyter_text>How many length 10^5 order of magnitude transcripts?<jupyter_code>! grep -P len=\\d\{5} Trinity.fasta |wc -l<jupyter_output>8917<jupyter_text>How many length 10^4 order of magnitude transcripts?<jupyter_code>! grep -P len=\\d\{4} Trinity.fasta |wc -l<jupyter_output>9598
{'fraction_non_alphanumeric': 0.158963282937365, 'fraction_numerical': 0.025485961123110152, 'mean_word_length': 3.5680473372781063, 'pattern_counts': {'":': 0, '<': 10, '<?xml version=': 0, '>': 10, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '3', 'dir': 'jupyter-structured-clean-dedup', 'id': '70237', 'license': 'MIT', 'n_tokens_mistral': 1127, 'n_tokens_neox': 1064, 'n_words': 172, 'path': 'notebooks/010_trinity.ipynb', 'repo_name': 'czbiohub/sequence-localization', 'size': '2315'}