Methods and systems for processing polynucleotides

A composition comprising:

• a plurality of droplets, wherein a droplet of the plurality of droplets comprises:
• a gel bead having a plurality of barcode molecules attached thereto,
• wherein the plurality of barcode molecules comprises:
• (a) a first barcode molecule comprising a nucleic acid barcode sequence, wherein the first barcode molecule is hybridized to a first analyte, wherein the first analyte is not mRNA and is not hybridized to the first barcode molecule via a poly-T sequence, wherein the first analyte comprises a clustered regularly interspaced short palindromic repeat (CRISPR) ribonucleic acid (crRNA) or a single guide ribonucleic acid (sgRNA);
• and
• (b) a second barcode molecule comprising the nucleic acid barcode sequence, wherein the second barcode molecule is hybridized to a second analyte, wherein the second analyte is mRNA and is hybridized to the second barcode molecule via a poly-T sequence,
• wherein the first barcode molecule and the second barcode molecule further comprise a random N-mer sequence.

A composition comprising:

• a partition comprising a bead having a plurality of barcode molecules attached thereto, wherein the plurality of barcode molecules comprises:
• (a) a first population of barcode molecules each hybridized to mRNA via poly-T sequences, wherein barcode molecules of the first population of barcode molecules each comprise a barcode sequence and a random sequence;
• and
• (b) a second population of barcode molecules each hybridized to an analyte comprising a clustered regularly interspaced short palindromic repeat (CRISPR) ribonucleic acid (crRNA) or a single guide ribonucleic acid (sgRNA) via a sequence that is not poly-T, wherein barcode molecules of the second population of barcode molecules each comprise a barcode sequence and a random sequence;
• wherein barcode sequences are constant among the plurality of barcode molecules and random sequences vary among the plurality of barcode molecules.